How to remove duplicate dynamic placeholders from Final Layout using SPE?

Firstly, you can filter the renderings returned before you get to a ForEach-Object, by using a Where-Object (my regex skills are limited, so I've just copied yours):

$Renderings =  Get-Rendering -Item $CurrentItem -FinalLayout | Where-Object {$_.Placeholder -match '(-{[0-9a-fA-F]{8}[-][0-9a-fA-F]{4}[-][0-9a-fA-F]{4}[-][0-9a-fA-F]{4}[-][0-9a-fA-F]{12}}-0)'}

Then you can build an array of your duplicate criteria (in your case the combination of placeholder and datasource). If a value is already in the array, you can remove the rendering.

$UniqueValues = @()
$Renderings | ForEach-Object{
    $Identifier = -join($_.Datasource, $_.Placeholder)
        If($UniqueValues -Contains $Identifier){
            Remove-Rendering -Item $CurrentItem -Instance $_

        }
        else{
            $UniqueValues ,+= $Identifier
        }

}