Fast forwarding works in bsnes without affecting the real time clock, so that can't be the case.
Sure it can, that's why I said it was hard coded logic, not part of the emulation. If it doesn't cause any glitches, then we can go ahead and remove that logic.
Edit: Done, knock yourselves out: https://dl.qwertymodo.com/snes9x.zip
Edit 2: Just tested, when fast-forwarding, the "game time" counter will advance at the fast-forwarded rate, but the clock remains synced to real-time. So, for instance, if it's 10:00am and I have played for exactly 1 hour, and I hold the fast-forward key for exactly 1 real-time minute, the clock will report that it is 10:01am, but I have now played for 1:14 (give or take, depending on your system speed).
I'm not sure if there is anything in the game that can be exploited by doing so, but there you go.