This might be the sort of thing you want to investigate for yourself.
I don't recall it in the usual discussions (while the classic nes/famicom mini series dominates discussion there then there are a few others, some even using the homebrew emulator pocketnes as it was made public domain https://waxy.org/2004/07/jaleco_borrows/
) but it very easily could have flown under the radar as most were content to use the pocketnes or HVCA emulators instead.
Anyway first easy option is grab a chunk somewhere in the middle of the original NES ROM and search for that in the GBA ROM. You tend not to gain much for compressing NES ROMs and I have rarely seen anything obfuscated or too radically altered when it comes to NES stuff (contrast to Sega of that era, and arcade/MAME stuff to this day in some cases). If you don't get it at first try a few others.
Whether they would have used an emulation scene/flash cart scene style dumped ROM in their GBA effort I don't know - while Nintendo were notably using the ines header in some of their later stuff ( http://archive.nes.science/nesdev-forums/f3/t4412.xhtml
and also notes a few others that used pocketnes https://www.eurogamer.net/articles/2017-01-18-did-nintendo-download-a-mario-rom-and-sell-it-back-to-us
) then back then there was still unknown formats being used that comprised dumps of the various banks stored how they will on occasion.
You might even find it in a dump of RAM, and RAM dumps can be a way to get around any compression or obfuscation (NES ROMs do just about fit in GBA RAM a lot of the time).
Beyond that I would probably start playing with the running code; an emulator referencing a ROM will look quite a bit different to a native program referencing assets when you start peering into the code, especially something as far apart in general theme of operations as the NES and GBA.