CTRNAND is a partition in NAND. Both sysNAND and emuNAND have a CTRNAND partition (given that emuNAND is a direct copy of sysNAND).
Replacing SecureInfo_A in sysNAND without A9LH would definitely be a brick. Placing SecureInfo_C wouldn't, I don't think, given that I assume it's just a part of the loader patch to use it instead (correct me if I am wrong) meaning that if you weren't in a CFW environment it would be ignored. You shouldn't touch sysNAND though, unless you have A9LH and recent backups.