If you are talking about legit .cias then forget about transfering NNIDs. Legit CIAs are not bound to your NNID they are stored locally on your 3DS. If you system transfer you can not redownload them from the eShop, because the games are not listed as bought on the Nintendo eShop servers.
It doesnt matter if you unlink NANDs (if you even have emuNAND that is) and transfer NNIDs, because system transfer doesnt transfer tickets.db, where the tickets for the legit CIAs are stored - once again - locally. You would have to redownload them from the eShop, but as mentioned earlier you do not possess the rights to redownload them, becuase you have not bought them legally on the eShop