To some extent this is probably the case, especially with that GBA emulator. An NES emulator for the GBA isn't quite a miracle but it would definitely make the poor little 16MHz ARM in there sweat.

It was probably only semi-deliberate, though. Even more than for hobbyist emulators, the point of these was to play games - and in these cases, some specific games too. And for most games, most of these inaccuracies are going to be pretty imperceptible in practice.

So if I were the poor Japanese salaryman entrusted with making this emulator, I'd start by implementing the NES hardware in the simplest, most obvious fashion, and only go further where necessary to get these particular games running. It just so happens that, in emulation, more often than not "simplest and most obvious" also usually translates into fastest.