The topic covers it I guess. Just wondering the best way to detect whether or not something is running on an emulator rather than real hardware ? (in code I mean, obviously eyes would suffice otherwise 
You can`t, unless you remember have you started UAE or not :-)
Even FPGAs are also kind of emulated hardware, just in different way.
Well, why would you care? Performance would be higher if its 68k JIT emulated programe under OS4 or MOS, but then again now with JIT enabled UAE this might change to be not that significant difference.