It's plausible that they might do this sort of thing, but don't get your hopes up. Here's why it's plausible:
-The GBA carts are, in fact, EEPROM. Or so say the flash linker communities.
-The Japanese FR/LG/Em carts have about 6MB of unused space; enough for a couple hundred new Pokémon, new moves, possible hold items, etc.. The English carts have even more unused space. Japanese Ruby/Sapphire are jam-packed to the top, so we can rule out that they'll receive an update, despite the fact that the English versions have lots of unused space.
-The Pokédex/movest/art/etc. data are based on lists of pointers, so all they'd need to do is extend those lists and flash the new data into the unused space. No need to overhaul the actual executable code. What dver suggested was basically a naïve, oversimplification of this, since out-of-range pointers (pointers to pointers, rather) all direct to Missingno.
Despite this, don't get your hopes up. Nintendo's never done any significant form of update to any existing product, so there's a good chance they won't do it this time, either. What would be more likely is a new fourth-gen RPG on the GBA, perhaps a G/S/C remake. (don't shoot me! XD)
