I have a feeling that 3DS flash cards won't be popular. If Nintendo is going to force updates on the end-user as rumored (even with the 3DS turned off apparently), it's going to be a pain in the ass for modders. Whenever Nintendo comes out with new official firmware, the mod users will usually avoid installing Nintendo's new firmware until the modders tweak their mod so that it is compatible with Nintendo's latest firmware. But if modders no longer have the option of declining a Nintendo update, they're fucked until the modders release a new version of their mod.
Just look at the PS Jailbreak situation. The modders still haven't made that compatible with the latest official PS3 firmware I believe. And better yet look at the PSP-3000 situation. If your official PSP firmware is above v5.01, you can not load isos off your PSP-3000. You can however homebrew enable ANY PSP (even PSP-3000 and PSPgo with v6.31 firmware) with the right methods. But it's not homebrew that is a threat to the PSP, it's the iso loading. So mission accomplished for Sony on the PSP front (as of late). There is plenty of PSP piracy among those with older PSPs with old firmware but Sony can't do anything more than they already are to prevent piracy on older hardware.
Personally I think there is a place for homebrew. It is in Nintendo and Sony's interest to block DS Rom/psp iso loading apps and certain homebrew apps (ie. allowing a SNES emulator on their 3DS would indirectly cut into Virtual Console sales of SNES games). However the harmless homebrew apps (ie. xvid/divx players) bring a lot of value to the PSP and DS. Plenty of PSP-3000 users with updated firmware love using homebrew even though they can't take advantage of ISO loading.
