This will sound horribly selfish but NO NO NO NO NO! Keep the mp3s!
GYM files are inferior because 1) no GYM player has 100% accurate emulation of the YM2612 and PSG, and most GYM players use the same emulation core (the one from MAME). 2) GYM files with a lot of PCM (DAC) audio occasionally end up bigger than mp3s if they are recorded for the same length of time. 3) This may be just me being a purist, but the "softer" analog output of the real Genesis (headphone jack) is very preferable to the sharp, hard sound of a GYM player at 44kHz. Also since the PCM audio is typically at a low sample rate in the game (usually 8 or 16kHz) it gets all noisy when upsampled to the 44kHz frequency. 4) This is arguable, but there seem to be tempo problems with some GYM rips, I don't know if this is a weakness of the file format or just the players/emulation.
Either way though, I do suppose that a GYM is still better than a VQF
If it's space concerns, I recommend encoding the mp3's at 96kbps 32kHz... there's no reason to use 44kHz encoding, and you will get significant savings in file size too (should be same size as a 96kbps VQF).