You probably won't be able to decrypt emuNAND and dump your own eShop games if you unlink the NANDs. This is a known problem with CTR Multi Decryptor but there is no information as to whether the same problem exists with rxTools, it likely does though.
Additionally, you won't have any of your legit eShop stuff on sysNAND anymore and you'll have to boot into emuNAND even when you just want to play legit eShop purchases.
Other than that, there are no notable disadvantages so if those don't bother you then go ahead and unlink.
My internet settings. Do tranfer over. And yes im mobile right now
You can already have different internet settings, by just filling up the internet connections on the sysNAND with fake ones it won't transfer over settings from emuNAND.