Hello,
Finally I decided to write my own solution which can be manually started after each Nintex update or scheduled via windows task scheduler:
Nintex feature hide script:
#***********************************************************************************************************
# Hide Nintex features from the UIÂ Â - Csaba Sztancsik (2015)
#***********************************************************************************************************
$FeaturesDefinition = "E:ScriptsNintex Features.csv"
$LiveMode = "Yes" #Yes to make changes or No for simulation and log creation only
#***********************************************************************************************************
# You do not need to modify anything below this line
#***********************************************************************************************************
asnp *sharepoint* -ea 0
$NintexFeatures = Import-Csv $FeaturesDefinition -Delimiter ";"
$SPServers = (Get-SPFarm).Servers | ?{$_.Role -match "Application"} | %{$_.Address}
$ModifiedFeatures = @()
clear
Write-Host "Searching for visible Nintex features..."
Write-Host ""
Foreach ($Nintexfeature in $NintexFeatures)
{Â Â Â Â Â
   Try
       {
           foreach ($SPServer in $SPServers)
              {
              $FeatureXMLFullPath = "\" + $SPServer + """ + $Nintexfeature.'Feature Folder'.Replace("C:","C$") + "feature.xml"
              $FeatureXMLContent = xxml] (Get-Content $FeatureXMLFullPath)
              if ($FeatureXMLContent.Feature.GetAttribute("Hidden") -ne "TRUE")
                 {
                 Write-Host $Nintexfeature.'Feature Name' -Foregroundcolor yellow -NoNewLine
                 Write-Host " is not hidden on server " -NoNewLine
                 Write-Host $SPServer -ForegroundColor Yellow -NoNewLine
                 Write-Host "   Hiding feature... " -NoNewLine
                 $FeatureState = $FeatureXMLContent.Feature.GetAttribute("Hidden")
                 if (!$FeatureState) {$FeatureState = "Hidden Attribute was not exist"}
                 $FeatureXMLContent.Feature.SetAttribute("Hidden", "TRUE")
                 if ($LiveMode -eq "Yes") {$FeatureXMLContent.Save($FeatureXMLFullPath)}
                 $FeatureXMLContent = xml] (Get-Content $FeatureXMLFullPath)
                 #Removing Activation Dependencies
                 $FeatureXMLContent.Feature.ActivationDependencies.RemoveAll()
                 if ($LiveMode -eq "Yes") {$FeatureXMLContent.Save($FeatureXMLFullPath)}
                 $Properties = @{
                        'Server Name' = $SPServer
                        'Feature Name' = $Nintexfeature.'Feature Name';
                        'Feature Old State' = $FeatureState;
                        'Feature New State' = $FeatureXMLContent.Feature.GetAttribute("Hidden");
                        'Activation Dependencies Removed' = "";
                        'Modified at' = Get-Date -format "yyyy.mm.dd HHss"
                       }
                 $FeatureObject = New-Object -TypeName psobject -Property $Properties
                 $ModifiedFeatures += $FeatureObject
                 if ($FeatureXMLContent.Feature.GetAttribute("Hidden") -eq "TRUE") {Write-Host "OK" -ForeGroundColor Green} else {Write-Host "Error" -ForeGroundColor Red}
                 $FeatureState = $null; $FeatureXMLContent = $null
                 }            Â
              }
       }
      Â
       Catch
       {
           Write-Host $_.Exception.Message -foregroundcolor cyan
       }
}
if ($ModifiedFeatures)
 {
 $ResultsFullPath = (Split-Path $script:MyInvocation.MyCommand.Path -Parent) + "Log_NintexFeatureModification_" + (Get-Date -format "yyyy-mm-dd_HH_mm_ss") + ".csv"
 $ModifiedFeatures | Select 'Server Name','Feature Name','Feature Old State','Feature New State','Modified at' | Export-Csv $ResultsFullPath -Delimiter ";" -NoTypeInformation
 $ModifiedFeatures
 }
Write-Host ""
Write-Host "Script finished."
Nintex Feature definition csv:
UI Name;Feature Name;Feature Folder;Feature ID;Activate;Activation Order
Nintex Workflow 2013;NintexWorkflowContentTypeUpgrade;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexWorkflowContentTypeUpgrade;86c83d16-605d-41b4-bfdd-c75947899ac7;True;01
Nintex Workflow 2013;NintexWorkflow;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexWorkflow;0561d315-d5db-4736-929e-26da142812c5;True;02
Nintex Workflow 2013 InfoPath Forms;NintexWorkflowInfoPath;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexWorkflowInfoPath;80bf3218-7353-11df-af9f-058bdfd72085;True;03
Nintex Workflow 2013 Web Parts;NintexWorkflowWebParts;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexWorkflowWebParts;eb657559-be37-4b91-a369-1c201183c779;True;04
Nintex Workflow 2013 Reporting Web Parts;NintexWorkflowEnterpriseWebParts;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexWorkflowEnterpriseWebParts;53164b55-e60f-4bed-b582-a87da32b92f1;False;05
Nintex Forms Prerequisites Feature;NintexFormsSitePrerequisites;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexFormsSitePrerequisites;716f0ee9-e2b0-41f0-a73c-47ed73f135de;True;06
Nintex Forms for SharePoint List Forms;NintexFormsListSite;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexFormsListSite;202afc3c-7384-4700-978d-6da3d3cce192;True;07
Nintex Forms for Nintex Workflow;NintexFormsWorkflowSite;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexFormsWorkflowSite;ac8addc7-7252-4136-8dcb-9887a277ae2c;True;08
Nintex Workflow 2013;NintexWorkflowWeb;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexWorkflowWeb;9bf7bf98-5660-498a-9399-bc656a61ed5d;True;09
Nintex Workflow 2013 Enterprise Reporting;NintexWorkflowEnterpriseWeb;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexWorkflowEnterpriseWeb;2fb9d5df-2fb5-403d-b155-535c256be1dc;False;10
Nintex Workflow - Nintex Live Catalog;NintexWorkflowLiveSite;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexWorkflowLiveSite;54668547-c03f-4bb5-aaab-d9568ebaf9c9;False;11
Nintex Live Forms;NintexFormsLiveSite;C:Program FilesCommon Filesmicrosoft sharedWeb Server Extensions15TEMPLATEFEATURESNintexFormsLiveSite;23fce797-ac15-4451-b8da-cf8ac6de6912;False;12
Nintex Activation script:
param
(
 # Absolute URL of the site
       fparameter(Mandatory=$true, ValueFromPipeline=$false)]
 Nstring]$SiteUrl
)
#*********************************************************************************
$FeaturesDefinition = "E:ScriptsNintex Features.csv"
$LiveMode = "Yes" #Yes to make changes or No for simulation and log creation only
#*********************************************************************************
Write-Host ""
Write-Host "Checking prerequisites..."
asnp *sharepoint* -ea SilentlyContinue
# Content database validation - Skip this part if you don't want to dedicate a content DB to this Nintex site
$DB = (Get-SPSite $SiteUrl).ContentDatabase
if ($DB.SiteCount -gt 1)
 {
  Write-Host ""
  Write-Host "WARNING: " -ForegroundColor Red -NoNewline
  Write-Host "The site must be moved with Move-SPSite command to dedicated content database prior Nintex activation." -ForegroundColor White
  Write-Host ""
  Write-Host "! Moving the site will cause impairment for the site object and requires IIS Reset, this must be communicated to site owners" -ForegroundColor Yellow
  Write-Host "! You must create a Nintex Workflow database prior Nintex activation and the Workflow database must be connected to the SharePoint Content database where the site moved." -ForegroundColor Yellow
  Write-Host ""
  Write-Host "Please handle these steps manually, then activate Nintex with the " -ForeGroundColor White -NoNewline
  Write-Host " Activate-Nintex.ps1" -ForegroundColor Yellow
  Write-Host ""
  Write-Host ""
  ExitÂ
 }
# End of content database validation
$NintexFeatures = Import-Csv $FeaturesDefinition -Delimiter ";" | ?{$_.Activate -eq "True"}
Write-Host "Activating Nintex features on site " -NoNewLine
Write-Host $SiteURL -foregroundcolor cyan
Write-Host ""
Foreach ($Nintexfeature in $NintexFeatures)
{Â
   Write-Host "Activating " -NoNewLine
   Write-Host $Nintexfeature.'Feature Name' -ForeGroundColor Yellow
   Enable-SPFeature -Identity $Nintexfeature.'Feature ID' -URL $SiteURL
}
Write-Host ""
Write-Host $SiteURL -NoNewLine -Foregroundcolor White
Write-Host " completed." -foregroundcolor green
Write-Host ""