Yes... and no. There are two things that those games check for: 1. system version and 2. game updates. The answer to both (on emuNAND) is CIAs.
The game needs to check for a certain system version to run. If it notices that the system version is lower than what it requires, it doesn't start (and if it's a cart, it will prompt you to update!). You can "cryptofix" a CIA game to remove this check. Of course, you can dump your own games, convert them to CIA and apply the cryptofix yourself... but the majority of people will just download a cryptofixed CIA from the Internet. How you deal with the morality of that is up to you.
The same goes for updates. You can install updates as CIAs and the game will recognize them. This even applies to games on cart, not just to eShop games or installed CIAs, that can boot without the need to cryptofix them. Again, you have to draw the line in terms of morality and such.
Obviously, emuNAND is not a perfect solution for the N3DS right now. You have to weight what you value more: CFW support or online features. I'll choose the former any day, but it seems that you value the latter most, and that's fine. The good thing about having kernel access is that downgrading will be much, much easier in the future, so you can always install an emuNAND if things get better for it.
