I don't actually own a handheld, but I've been researching them a lot. And this discussion of scaling got me interested, because I care a lot about that sort of thing.
So I did an experiment.
1. Set my desktop monitor to 6480x480
2. Run RetroArch
3. Set an NES emulator to crop the overscan area.
4. Set my scaling setting to both under and overscale
In both tests I did not see any shimmering effects. As I expected, because why would I? It's being integer scaled. That said, the overscaling was severe on 640x480 set to overscale 224p and thus unplayable.
>Integer Y scaling
>Smart scaling
These are not options on desktop RA as of the 2024 version I use. But I would assume the Y scaling without X is the issue here.