I have the 9C and 45FS, both with the thumb safety. I prefer the safeties because I shoot 1911s a lot. I like to stay in the habit of working the safety.
I shoot 1911 and P35 style pistols, drawing with the thumb on the safety and dropping it on target is a natural for me. Wife has a 9c, same thing, absolutely no problems with the safety, it keeps all motor skills identical, that's a plus.
Besides, one extra safety is a good thing, just ask the big "G" shooters with a hole in their foot.
Love my MP9C. The Apex aftermarket parts fit like a champ and are a definite improvement. If you are truly looking for a compact 9, the 9C really isn't w/ the double stack mag. It's not bad, but it is definitely in a different category than say the Kahr CM9, which I also own.
What is nice about the M&P Compacts is they are small enough for CC yet large enough where you can go to the range and enjoy shooting a couple hundred rounds at normal pistol distances. A Ruger LCP is way smaller but it is not a shooter.
The thumb safety is preference. I bought a 45C with the TS and hated it so off it came. 9C was purchased sans TS. Like the TS on my 1911, but on the M&P I think it is wimpy and worthless.