Are the fid-filenames all unique ?

Yes.

I figured out that the main playlist-fid is '/drive0/fids/100', does it also contain references to fids in /drive1/fids ?
I have only got a one drive system, so I cannot test this...

Any fid can live on either drive (it depends which has less space when it's written). I think in theory fid 100 can end up on drive 1. A playlist fid just contains references to other fids -- any fid is looked for on drive 1 if it's not found on drive 0.

Peter