I'm also guessing a lot of the world's C99 code has dependencies beyond the just the compiler that Visual Studio won't support without some effort. "Just compile it as C++" is not a good answer, but I wouldn't be surprised if "just install Cygwin" often is.
Forcing legacy code to stay woefully out of date to support a single vendor's stubbornness, perpetually growing its maintenance burden as the rest of the world moves on. Hooray for the Microsoft way!
C90 isn't going away, and it's not Microsoft's fault. Many C compilers still support 1st edition K&R style for a reason — old C code is going to stick around, and it's probably not going to change much, let alone in any way that needs C99 features.
Ad 2) If there is support for features there will be people using them.