I think that if it gets so bad that Nintendo stops making profits (which is not the case right now by any means) they should capitalize on piracy like Apple did with iTunes.
How?
Release an official flashcart or two, one that uses MicroSDs and one that uses nand flash. Have a GBA addon for both. This flashcart, being from Nintendo, has perfect playback, including single- and multi-cart play.
Start a download service like iTunes, offering super-encrypted roms for about $10 less than their retail. This way they don't have to spend money on the hardware and can spend more on encryption.
Have their official flashcarts play unencrypted (normal, like an MP3 on an MP3 player) roms and encrypted ones from the download service (like AAC on an iPod). Basically, normal roms are to MP3s as the encrypted ones I proposed are to AAC.
They could have official media software on the flascart, letting it play MP3s, wmas, MPG1s, dpgs, ect, But that's secondary.