My guess is that only the online ones, like Animal Crossing: New Leaf or Mario Kart 7 will have spotpass updates that block these flashcarts. Currently, the sole purpose of these spotpass updates is for bugs, and I remember one of them for MK7 being an update that removes an exploit in one of the races. Without updates like these, and much like system updates, all online functions are restricted, only available once you've updated. While I'm sure there can be patches, it's a real inconvenience to have to patch games like that. Perhaps the makers of Gateway and other potential cart makers can program it so no updates from the big N are made available. Of course, if you're planning on playing online, you probably shouldn't use a flashcart anyways.
But yeah, flashcarts flourish once the life of the console is almost over. I bet the Letterbomb exploit for Wii is easily patchable, but Nintendo didn't do anything about it. They've shut down WiiConnect24. They don't care if the Wii is hacked. When the 3DS is almost dead, they'll remove patches for that, too. That's why I'm not buying a flashcart until:
1. Backups are made easier to dump from the cart. It's easier for me to be able to do something like dump a disk from the Wii to a USB stick, and I'm sure there'll be a way to get the data from the cart to an SD card, which will make things a hell of a lot easier for me instead of carrying around all my cartridges. I don't want to have to download backups.
2. A softmod can be made from a flashcart's exploitations so I can just run backups modified from an image to a usable format to the SD card, and on the 3DS from there. No need for a flashcart by then, but hopefully they'll be less expensive by then.
3. Homebrew in general, such as emulators (that will hopefully let me run my GBA backups) or media players (namely video) are made available by flashcart, but if Gateway's cart is made available by an exploit, I'm sure the same thing can be done by emulating the encryption of the 3DS's software by making a piece of software for PC that allows for the entry of vital 3DS data, such as s/n or whatever it may use for the encryption to be used to use the image to recreate the software.
4. Such a process allows for the creation of a homebrew loader for 3DS. That would be so great...
I love how you assume that a soft mod would be made via a flashcart. It can be probably done without them, looking just at the guys at 3D Brew. We won't know for sure really until a few years go by, but I honestly want a scene similar to the Wii to snuff out flashcart businesses. For the DS, you needed them, since there wasnt any external media slots on it, but on the 3DS, along with some of its more sophisticated Firmware aspects, makes it a much better target for a all in one hacking package (including an SD card, excluding a flashcart), after you install (which just may be a game, like the current save exploit). Of course, there is just one problem... The 3DS is just extremely hard to hack in a substantial way in general, and honestly the fact that gateways team said they were currently stuck on 4.5 makes a bit suspicious on what exploit they are using (they said they were exploit based, didnt they?).