Please get the latest driver directly from Intel, not from your notebooks maker or anywhere else.
This very much looks like an older driver issue which usually HP users reported (but probably affects others too). Generally support for Windows on that Intel GPU is far worse than on Linux or for other GPUs.
Also as @Leo121 pointed out correctly: That game probably requires those system files.
If you don’t have a 3DS you can’t dump the files and / or legally play it.
If you also happen to have Zelda: OoT I’d recommend dumping that on a friends 3DS and testing it on Citra.
OoT does not require the system files and could be used to check if your graphics driver works properly.
(Actually we should probably pack some 3DS homebrew for this…)