I'm looking for a 2.1 powered speakers system for my HTPC, and due to severe space limitations I will have to place the sub unit inside a metal cabinet (which the TV sits on). Is that something that's generally not recommended? Will that degrade the sound quality or create noisy vibrations?
It will work OK, as long as the magnet in the speaker is shielded, it won't distort the TV picture.
Low frequency is non directional, so that will work OK.
As far as mechanical vibration, we can't see your cabinet. We could not possibly know.