Most Zelda hacking is either for the N64 efforts or NES and SNES efforts. Save editors/info splurgers tending to be for general RPGs where such things are more important rather than Zelda where "have hookshot" is a simple cheat rather than something that might benefit from stats and inventory editing.
Your best bet at finding something is to see if there is a "got all kinstones" cheat* out there, or better still have kinstone from ???? with list of possibles cheat.
*hopefully said cheat does not rely on the game having a separate value for that particular feat -- some games rather than doing max health - current health does it equal 0 will have something that merely notes full health is in play, have seen similar for stuff like this before.
It might not be the worst cheat to find either, not basic infinite money cheat but also not too drastic. I imagine it is going to be flags (done and not done, though "not seen, seen but presumably did not have stone and done" might be an option -- think pokemon). I would start by having a save(preferably savestate) with some kinstones and standing by one to do the deed with. Before doing it then do a few rounds of value has not changed (gets rid of some background timers, animations, music... that might alter the memory even when idling), do the deed, search for something that has changed, then more rounds of not changed if that is helpful. If you are lucky you will find it from that, though flags like this are annoying which is why you might when want to revert to the old save(state) before you did the deed, search for something that changed (it would presumably be back to not done form) and repeat until you get it or can get the number low enough to brute force.
I imagine the list of kinstones done are one big list (in an ideal world then all being 1 byte values one after the other --
https://www.thonky.com/zelda-minish-cap/kinstone-fusion says 100 kinstones which is an almost acceptable amount of memory to waste on the GBA, though it could pack it in smaller -- 1 bit for done or not done makes it considerably smaller at the annoyance of having to decode it**). If this is the case then you could trip the remaining ones if you wanted to (even more so if that guide is correct and some might be gated off by various gameplay actions), or maybe figure out which is which -- order in game is a reasonable bet but order they were added in development*** is the better one, I can't remember if there is an in game encyclopaedia or anything like some RPGs have bestiaries that might give a clue that could work in light of this (I imagine you would have used it but info like this can be combined).
Anyway once you have one you can check nearby locations and see what goes, or indeed go to another kinstone fusion option (the main town as it were having several in close proximity). You might then also compare a new game save to your basically full save to get an idea of the start and end of the table****, though that is probably easy enough to find experimentally, you might also get some idea as the internal potentially hidden ordering (while I might not bet on the overall order I would bet on each section in the game itself generally following another rather than complete random)
If you are not familiar with cheat searching then my usual link is
https://web.archive.org/web/20080309104350/http://etk.scener.org/?op=tutorial , it is a bit old but still very good (and applies to most consoles, not just the GBA it covers).
https://doc.kodewerx.org/hacking_gba.html if you need to know what is available for GBA cheats. It is not so bad for emulators (or indeed savestates you can edit with a hex editor) but if you find yourself needing to alter several dozen individual bytes then you would want to look up "slide codes" which are constructions aimed at doing repetitive things separated by fixed/easily calculated values).
**on the NES then wasting 100 bytes of memory gets you fired, and while the GBA has an awe inspiring sub 300 kilobytes if you add everything up (
http://problemkaputt.de/gbatek.htm#gbamemorymap ) then that is still a drop in the bucket and if it also spares you having to fiddle around with shifts and masks (instead something like take base location add character ID multiplied by 8 and look at the value there, 1 is done, 0 is not done) then yeah.
***there is an old game dev adage of make the first level(s) last -- by that point you hopefully know your engine, know its limits, know what works for the game and thus can have that brilliant first level to hook people and lazy reviewers in. While kinstones were probably an afterthought then I am still not betting against something happening along those lines, or the devs going alphabetical (in Japanese) to get it done.
****while useless extra space might be because 128 is easier for computers than 100 to deal with then this is also how various cut and hidden content gets found, not sure it is much use here but if you find yourself doing similar with an inventory cheat, character selection cheat, level select cheat, pokemon seen/caught cheat or similar in the future then it becomes more valuable.
