SNES had better sound capacities than the GBA, so its normal that it suffers.
And FF6 arguably pushed the audio hardware to its limit in that aspect.
But if you compare other games that were ported from the SNES, they all had some slight issues. I haven't tried this version yet, but I won't be surprised whatsoever by the lacks in audio.
FF5 and FF4 barely suffered in comparison, possibly because the songs themselves where less intensive, but you'll still notice that some of their songs lack an instrument here and there, but nothing too terrible.
Even Zelda, one of the first SNES-2-GBA ports went through downsizing of their instruments. Remember how 'orchestral' the SNES Zelda was?