I want to say that I don't want to come across as pushy and ungrateful for anything you've done. But since you asked then I assume you want to know- Yes, absolutely. IF you feel comfortable putting the time and effort into it and want to do it, then i'd absolutely welcome it. I have the utmost respect for you and your work. With your hack (which I use alongside the color restoration), FF6A becomes an actually pretty great port with some nice bonus content.
I'm particularly interested that you mentioned audio panning and stereo. I was aware that you removed stereo sound in your hack, which the readme mentions. Is your comment implying an update could be made to restore this now? That would be well worth it. I know the GBA only has one speaker, but I usually use stereo headphones or similar when playing GBA games. It's also cool that you mention lag could be further reduced as well, even with the improved sound quality.
One question- is there anything that can be done about the way the music loops during the final boss' forms? On the SNES, the music seamlessly crossfade to the new track as the boss switches forms, waiting for the track to finish before swapping to the new one. On GBA though the transition is more immediate, it just loads the new track as soon as the form is destroyed and doesn't wait for the song to finish. I assume it's not easy to fix, but I thought i'd ask if you knew anything.
The only reason I can think of not to do an update is if you had plans to fix the sound in other GBA ports of SNES games or something like that. Or of course if you don't want to. Real life also always takes precedence.
I don't think worrying about whether enough people download the newer version should be a factor in the decision. If you're really that concerned about exposure, you could contact one of the staff members here when it's done and see what they can do. Maybe they'll give it an exclusive news article separate from other hacks. But either way I still wouldn't let the worry that it won't get as much attention as the original release stop you from doing it.