To clarify, there are three main issues with trying to hack out the emulator in SCC-
1- they disabled ALL sound emulation in the port. Any music or sound effects you're hearing ingame are actually held in separate audio files that are being directly streamed by the DS (i've looked at a decompressed rom myself). It's the main reason why the game is so large (64MB) even though the original Sonic games never went over 3-4MB. The sound samples and music files are taking up large amounts of space. Suffice to say, they aren't using the Genesis sound hardware to output the sound like JenesisDS is. If you managed to insert another Genesis game into the collection to play, you wouldn't hear any sound since the collection isn't programmed to output sound unless it can read it from those files (and you'd have to hack, convert, and extract/insert your own music to hear anything). It should be noted that someone did manage to rip the roms out of the collection and run it on a PC emulator and they still had their original sound, but the DS collection can't play those samples. So it's useless regardless.
2- the roms in the collection were hacked in a minor way just to scale the graphics and fit the ring counter/timer/score. When you play them in a pc emulator, the graphics look a bit messed up. If you inserted a rom, you wouldn't automatically get better scaling than the JenesisDS emulator. You'd have to hack the roms themselves to be scaled properly.
3- SCC is indeed slower than JenesisDS. Playing Sonic 3 or Knuckles is very laggy unless you play without a second character onscreen. Still laggy though regardless. JenesisDS can achieve constant fullspeed in all the Sonic games. The glitches are rare and never really disturb you except the Lava Reef boss in S&K (and that's still manageable).
I would stick with JenesisDS. The sound may be slightly off and the games might have more glitches, but the games are far faster and don't lag much at all. If i had to pick, i'd just stick with JenesisDS. Too much speed was compromised in the port, and you wouldn't get any sound anyways.