> This doesn't seem to me to be evidence of deliberate anti-emulation features - just imagine a hastily written port by relatively inexperienced developers who don't know about these quirks

If it were one thing, maybe, but six things done in almost no or no other games repeated across (presumably) thirty ported games? Infinitesimally unlikely.

Also, these were done by Nintendo Japan - how likely is it that they're "relatively inexperienced developers writing hasty ports". These tricks would seem the hallmark of very experienced developers who know the hardware intimately.