Most likely the anti-AP system in will deploy will need patches, but not to the games, but to the firmware of the card itself. No doubt it will use the cpu to scan (or use from a list on known) AP against the image to build an "on-the-fly" patch to bypass the AP. Meaning if it is programmed to reconize AP type 1, the card will scan a rom looking for AP type 1 and automatically deal with it. They also might even be able to program the software so that even if the AP is type 1.1, if can reconize and deal with the protection on the fly. Look at how many games come out with AP that are solved using methods already done. This is just speculation on my part, but would make sense.
I hope the GBA emulation gets more flushed out in future firmwares, but given SC methods of keeping thier cards up-to-date, I would be suprised for them not to improve it.
I already pre-ordered one myself, love my AK2i, but I do have some reservations about depending on a 3rd party to keep the software up-to-date. I mean he has done an awesome job, but considering he does not make the hardware, will he always make the software.
The only question I have, which has never been anwsered (or I am blind), is does it run DSi Enchanced/Only games using the DSi features (which may never been worthwhile, but that is not the point)?