It's the kind of thing that at this point in time will have absolutely no benefit, yet is the 'right' thing to do, so I would say 'yes', especially since I know of no emulator that is bothered by this.
(Background info: My custom Nintendulator Mapper DLL does honor the submapper field. If you were to set the submapper to 2, indicating the presence of bus conflicts, you would get the same result as in FCEUX. Which proves that the bus conflicts explanation was the correct explanation. There is at least one game (Cybernoid by Acclaim) that requires bus conflicts to be emulated, which is why emulating them is not just nitpicking.)