I've always suspected that Nintendo cares a lot less about PC emulation, than it does about mostly-chip-compatible knock-off hardware.
Think of those consoles you see at Walmart that claim to come with "100 games built in!" Those frequently contain chip-compatible designs of Nintendo's old hardware, and a library of ROMhacks of NES games (or the ROM from a single one of those 100-in-1 NES carts.) They're not emulating Nintendo ROMs; they're just running them, directly.
The manufacturers of these consoles never bothered to clone newer ones after the NES, because all the demand for these knock-offs seems to be some weird combination of nostalgia and clueless-parent value-purchasing (e.g. "oh hey, it has Super Mario Bros on the box! That game was great. My kids would like that!")
But the GBA is just as easy to clone the internals of as the NES is (ARM7 cores are just as easy to find—and cheap—as 6502s), and has a far larger library of games (~17000!) So if these companies could transition to a GBA chip-compatible design and still ship these NES ports, they'd increase value immensely, while still being able to put NES nostalgia on the box.
And so, for these ROMs that might have been just the thing to spark this switch-over, Nintendo went to some extra effort.
It would have been funny, had any of these knock-off manufacturers already finalized a hardware design based on tests with other GBA ROMs and started up their logistics pipeline to assemble consoles, had they flashed one of the NES Classics ROMs onto their new-off-the-line console, and realized that it was far more stringent than other games were about faithfulness to the GBA's architecture. It might be enough to kill a whole company.
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Of course, none of this ever materialized, because for some reason, the knock-off manufacturers are still just making consoles that are chip-compatible with NES games, rather than speccing out builds based on what chips have become equally cheap since then. Who knows why.