Just add another clause to the where filter:
$AllVMs = $FullVM | Where {-not $_.Config.Template -and $_.Name -notmatch "^VDI" } | Where { $_.Runtime.PowerState -eq "poweredOn" -And ($_.Guest.toolsStatus -ne "toolsNotInstalled" -And $_.Guest.ToolsStatus -ne "toolsNotRunning")}