Since MySQL kinda treats databases like postgresql and oracle do schemas (i.e. you can do cross db joins and such in mysql) is there a real big reason to want to put them into the same db?
If not, you can leave them in separate dbs and they should be fine.
otherwise you're gonna have to do something to tell the table(s) with the same name apart, i.e. rename them and edit all the code that accesses them, which can be error prone.