You definitely do not want to bake the vinyl case portion of the floppy. I may have the baking temperature completely wrong (perhaps it really is only 110-120F?) for the 'cookie'/media part. I believe it should be baked against a flat (polished?) metal surface to prevent distortion, but again I could be completely wrong. (I suppose it could melt like an egg even if it is against a flat surface)
Baking tapes is done to remove moisture. Why not just throw the disks in with some dessicant (Damp rid comes to mind?) I bought some damp rid in preperation for reducing moisture in some umatic tapes that have laser show data digitally encoded. But so far the tapes play really well and I just dump the converted signals to HD based ADAT machine. Beta tapes faired poorly.