I have opened a ticket with Nintex for this.  As I have no way to determine where the Nintex licenses are being used without some kind of cumbersome manual tracing across so many sites and site collections.  

I know this is an old post, but maybe this will help someone.

You can locate you Nintex Forms in SharePoint Online using this PnP PowerShell:

# Connect to your SharePoint admin site
Connect-PnPOnline -Url "https://yourSPSiteName-admin.sharepoint.com/" -Interactive

$entitlementType = "<EntitlementType>Production</EntitlementType>"
$ProductionFormsCount = 0
$DevelopmentFormsCount = 0

# Get all site collections
$siteCollections = Get-PnPTenantSite

foreach ($SiteCollection in $SiteCollections) {
  $SiteCollectionUrl = $SiteCollection.Url
  try {
    #Write-Host "Trying to connect to: $SiteCollectionUrl"
    Connect-PnPOnline -Url $SiteCollection.Url -Interactive

    # Check if the web has a "NintexForms" list
    $nintexFormsList = Get-PnPList -Identity "NintexFormXml" 

    if ($null -ne $nintexFormsList) {
      Write-Host "Site: $SiteCollectionUrl"
      # Get all items in the "NintexForms" list
      $nintexFormsItems = Get-PnPListItem -List $nintexFormsList

      foreach ($item in $nintexFormsItems) {
        $formType = ""

        try {
          $xmlFile = Get-PnPFile -Url $item["FileRef"] -AsString

          if ($xmlFile -match $entitlementType) {
            $formType = "Production"
          }
          else {
            $formType = "Development"
          }
        }
        catch {
          Write-host -f foregroundcolor red "Encountered Error:"$_.Exception.Message
          <#Do this if a terminating exception happens#>
        }
        $fileLeafRef = $item["FileLeafRef"] 
        $splitString = $fileLeafRef -split "_"
        $listId = $splitString[1]

        try {
          $formList = Get-PnPList -Identity $listId
          Write-Host ("Form Type: " + $formType + ", List Name: " + $formList.Title + ", View Url: " + $formList.RootFolder.ServerRelativeUrl ) 
          if ($formType -eq "Production") {
            $ProductionFormsCount = ($ProductionFormsCount + 1)
          }
          else {
            $DevelopmentFormsCount = ($DevelopmentFormsCount + 1)
          }

        }
        catch {
          #Write-Host "List does not exist"

        }
      }
      Write-Host " "
    }
  }
  catch {
    <#Do this if a terminating exception happens#>
  }
}
Write-Host ("Production Forms Count: " + $ProductionFormsCount + ", Development Forms Count: " + $DevelopmentFormsCount)