If memory serves it shouldn't cause an issue - it's an x10 database that is, presumably, storing some data about the account but showing up in your cpanel. Far as I know cPanel counts it for the counter, but doesn't when it actually counts -your- databases, since it isn't actually set up to be yours.
I'm on paid but I've got a similar database, but when I accidentally tried to add a user to that one, it didn't allow it because I don't have permissions to the database.
For now I wouldn't worry about it, unless you get to 5/5 and it doesn't work. From what I gather, it'll actually let you get to 6/5 before it stops working, since that's when you'll have 5 that are actually yours.