It is the same emulator. The author of JenesisDS is even credited in the staff list option on the main menu. Look for Stephen Dittrich as head programmer on that. That's the same person as Lordus, the programmer of JenesisDS.
There are a few key differences in the latest JenesisDS and SCC-
1- SCC fixes the sprite/background priority issues seen occasionally
2- in SCC the special stages in Sonic 2 and 3K no longer appear as a glitchy mess
3- in SCC, the Lava Reef boss scrolls correctly and isn't obscured by the lava anymore
4- in SCC, the sound effects and music aren't emulated at all, but each individual track and effect is held in its own file when you unpack and look at the rom data. It's streamed via the DS hardware now instead of being inside the rom emulated. This is why the game required a 64MB cartridge even though the entire Genesis Sonic game collection only takes up a couple of megabytes
5- large rom support which allows you to play S3K and S2K.
6- SCC has slightly different looking scaling. Still looks like crap, but is a bit better
I would surmise the speed loss to be something to do with the new features. No one knows for sure. But there is no doubt that it is the same emulator updated and packaged as a commercial game. There is overwhelming proof that it's the same thing. And Lordus never released the emulator open source IIRC. Even if he did, he has the right to withhold later versions.
About 2 years ago, i talked to Lordus but then he mysteriously disappeared. We all thought he just moved on with life or something, but when SCC was announced, it was a heavy suspicion that SEGA just contracted him to develop for them. It turned out we were right. You don't need any more proof than his name in the credits. After that, it's obvious the game is running on the same emulator slightly updated.