I don't know about creating problems, but it's definitely a warning to make sure that set::network-name (or whatever it is) is the same across all servers. (Suppose there's a good reason why it warns you.)
Where's the point in having a Network with more than one name? Isn't that kinda irritating for the users?
User 1 is chatting on RelicNET and User 2 on DigitalNations, but they still are on the same network?
Give your SERVERS different names, not your Network.
Will it cause problems? That depends. One, is set::hidden-host-prefix the same on both? If not, you now have ban evasion problems.
There are also client issues. I use Klient. Klient allows you to list all the servers of a particular network. Now if I listed the DigitalNations servers under RelicNet, I suspect that when I connect and it sees "NETWORK=DigitalNations" it is going to become confused. I told it the network is RelicNet, but the server is telling me that is wrong.
You should have the same network name on all servers.