Supercard did stuff on the GBA and DS, and had several versions within that (golden sun and Rhythm Tengoku both featuring on the GBA and the DS) so you might want to clarify what you are doing there.
GBA supercards suck because the team cheaped out on the memory and consequently had to patch every game for speed (not a trivial task) using their software where every other flash cart used good enough memory and only had to do saves.
DS supercards that worked in the GBA slot needed patching because they were not designed to run from the GBA slot so needed some help directing reads and saves to the proper place. Near every new game needed patching, and later ones also started introducing anti piracy and other fun things. The GBA slot line was abandoned way before DS ROMs stopped being released as it was too much effort when everybody could just buy a cheap and cheerful DS slot device (in the time since the DS slot stuff had been figured out) that did not need as much effort to patch for. As far as hacks go I am not sure what the software uses to detect games -- some GBA slot DS focused carts used a straight up hashes which would change when you hack it (or even trim it really). Others might have used serials, certain hacking tools would also rebuild in ways that certain carts do not like.
I don't know that the GBA slot DS software did patching for ROM hacks, if it did though there are a bunch of formats and revisions of them (the xdelta one that I liked and pushed a lot had the
http://www.evanjones.ca/software/xdelta-win32.html one I used at first, and then xdelta official got a windows port and started being updated
http://xdelta.org/ and so there are two different versions of the concept out there, I am not sure what went with bsdiff in the end and then there are loads more that people used for all sorts of different things). If it is for the GBA then there were two main patch methods seen, though some also used the likes of xdelta and bsdiff in some cases. IPS and UPS were those and IPS is a nightmare with all sorts of crazy offshoots and UPS might not just be supported as it was not so easy to implement.
Short version. If you are using any kind of GBA supercard then do yourself a favour and upgrade to a real GBA cart if you want GBA, or a DS slot cart if you want DS. Supercard's DStwo, DStwo+ and now 4 in 1 should have a GBA emulator onboard which does pretty well too but in many cases a hardware flash cart is nicer. If you are using supercard software to patch hacks into games then stop that and use a more dedicated patcher (try a few).