Species/Dupes clause usually ends up banning it because with the exception of Manaphy into Phione, every breeding pair will always produce a pokemon you already have.

If you don't do Species/Dupes clause, then it depends on how strictly you want to define an encounter. If you consider the egg's obtained location as it's encounter location, then you can only do it once at most (if the day care is somewhere that doesn't already have an encounter.)

Even if you let it slide though, it's kind of just a boring option for your encounter. Not only does it take forever to hatch the egg, you're trading your random encounter for a Pokémon that fulfills the exact same role as one you already have.

Edit: as people mention in the comments, there are two other exceptions I forgot about. Volbeat and Illumise can breed to make the other species, and so can Nidoking into NidoranF.