It _probably_ won't make much of a difference, but if the emulator does scanline-based PPU emulation then you can expect to see timing errors at some point. One cycle doesn't sound like much, but if there's something like this:

$8FFD LDX #$FF
-
$8FFF DEX
$9000 BNE -

That's going to use about 255 more CPU cycles, more than a couple scanline's worth of CPU power.