Chuffed to bits
Yes. Hardware limitations.I see that the difference is much greater. It's just differences in sound hardware in both the GBA and the 3DS.
In GBA, the instruments are emulated. In the 3DS, the songs are streamed thus keeping the real sound of the instruments.
If the GBA tracks were not emulated but instead played using actual instruments used for ORAS, I'm sure it would sound similar, too.