GBA debuggers have been around for years and years now, though you will tend to find three in common rotation.
Those around for the longest might still be using VBA-SDL-H
https://www.romhacking.net/documents/361/ (that being a guide to tracing graphics)
https://web.archive.org/web/20130215155212/http://labmaster.bios.net.nz/vba-sdl-h/
It sort of is command line based (or at least has its own internal command line equivalent) but has abilities that some others might not have/are normally only seen on PC and high end NES stuff like
https://fceux.com/web/help/CodeDataLogger.html (fceux being the gold standard for console debugging, that which everything else is measured against, PC being the only thing that beats it, indeed PC with stuff like IDA blows it out of the water).
no$gba has long featured a top rated debugger and a few years back became free (was paid before, mainly as several devs of GBA and DS games paid for it).
http://problemkaputt.de/gba.htm
http://problemkaputt.de/gbatek.htm is probably also the main reference for GBA hardware, though
https://www.cs.rit.edu/~tjh8300/CowBite/CowBiteSpec.htm#Graphics Hardware Overview
http://www.coranac.com/tonc/text/asm.htm also have good stuff and there is much more (most of which I linked in my hacking guide).
mgba
https://mgba.io/ is newer on the scene but the author of it does some really good stuff
https://mgba.io/tag/debugging/
Its debugger is like many modern emulators and farms it out to GDB (gnu debugger, people making gnu gcc, aka the main non Microsoft C compiler) which can then be spoken to by all manner of things
https://wrongbaud.github.io/posts/ghidra-debugger/
Ghidra
https://ghidra-sre.org/ if you are not familiar is one of the three main open source answers these days to IDA
https://hex-rays.com/ida-pro/ida-debugger/ which you might see some also use for this sort of thing (watch any hacking conference and if it needs a debugger chances are that will be the one used. I see it less for the GBA than I do DS, Wii and whatever other consoles people are looking at though).
https://rada.re/n/ and
https://x64dbg.com/ (which is primarily x86/x64 focused anyway, as will be the IDA free version).
There are a few more vintage emulators that can be used to do things but none of those have the feature set needed for this/comparable to the above (can be useful for certain types of hack though so some might still use them). VBAM
https://vba-m.com/ (a largely successful project to merge all the VBA forks that existed before and after the end of vanilla VBA, which would have included at least elements of VBA-SDL and VBA-SDL-h ) does have some GDB stub options as well last I checked but the others are probably better choices. I don't know what the tool assisted speedrun peeps are using right now but they sometimes make their own debuggers (it is kind of necessary to get anywhere real in such fields), though I normally save searching that when I am not hacking a system with a nice debugger.
There are also static options, and things you can do with simpler emulators (my primary method of finding palettes is to dump them from where they are at in game, possibly with some cheats to force a scenario faster, and search the ROM for it -- they are usually effectively random and relatively speaking very small so rarely compressed and that then means palette animations* which mostly mean search for the non animated fragments and dynamic/selectable palettes like some things had to account for GBA, GBASP and GB player screen options being the main pitfalls of that approach). Live memory viewing and register info (as well as live disassembly) are available in fairly stock versions of VBA and thus most forks as well but breakpoints for tracing a rarer concept save for their GDB stubs.
*Mr Driller 2 rainbow blocks and summon night swordcraft story saving swords glow effect being some nice examples.