Now, don't get me wrong,I do feel bad for users affected by these kinds of things, but after the first wave of gateway and clone related bricks, I don't understand why people continue to buy such 3DS flash cards especially when installing a CFW with auto boot EmuNAND is now do easily achievable without the need for any flash card. Granted, you may want a DS flash card in such a case to play all your favorite DS titles (I personally use an R4i gold card in mine), but DS flash cards have no risk of bricking your 3DS. I guess I'm just saying that I'm glad I held off on ever getting a Gateway especially when all those first bricks occurred.
One advantage I could see is that flashcards allow you to play games directly from Slot-1. Copy roms to microSD card and you're done, you can play them.
Granted, it is a bit more of a hassle when it comes to online play, because you have to mess with dumping headers from one of your games and apply them to your roms, when .cias will just work online without any problems and are pretty much undetectable (I read on here that there was still a way Nintendo could detect private headers used on the wrong game, for example Steel Diver header on SSB4, but they have yet to act on it.)
I mean, they both have their ups and downs, flashcards let you play the games right away just from putting them on your microSD card, but online play is a hassle and can be risky business.
.cias can take forever to install (several hours,
especially if you have a lot of games), but online play is pretty much guaranteed to work without running the risk of getting banned (I guess maybe unless they can check your 3DS's header and see if your 3DS is associated with a purchase of the game you are playing.)
Now, under normal circumstances, you would probably only have to install your .cias once and you're good, but sometimes you might have to re-install them a few times (I've fiddled with my setup a bit and had to re-install games a few times over the course of several weeks, which took a few hours every time) but the average user will probably only have to install them once.
There's also the advantage that CFW is almost completely free (you might need other things such as a DS flashcard or OOT/CN depending on your setup), while flashcards require you to spend money on buying their card. But I don't think the price should be considered when comparing them, because while flashcards have a high cost while CFW only has minimal costs, flashcards have the advantage of convenience, in a way.
Then you have >9.3 users which don't have a choice other than using a flashcard (Sky3DS), because nothing else will work.