No. Since Diamond/Pearl there is "Nicknamed" bit stored in individual values bytes, probably to allow dynamically changing the nickname when Pokémon was traded internationally using GTS. The name rater always sets this flag, even if you changed the name to species name.
However, this only applies to Diamond/Pearl, and games released after it. Before GTS that allowed online trades (well, technically Pokémon Communication Center also allowed trading, but it was Japan-only, so no issue here), there wasn't a nickname flag. The game determined if the specie was nicknamed in very simple way - if it had the same name as the specie in your name, it was assumed to be not nicknamed.
This obviously caused a problem when the Pokémon was traded internationally and evolved, but before fourth generation such trades were rare (before you ask, yes, Game Boy games allowed international trades, but only between versions using Latin alphabet).
Just for fun, the only Pokémon that couldn't be restored to original nickname in second generation was Porygon2, because you couldn't type "2" normally.
In fifth generation (not sure about sixth), there is the only way of removing nicknames I'm aware of, but it's probably not intended to be used in this way. There is a filter in a game (client-side, server instantly rejects such names, which is an issue with specie names like Nosepass) that automatically removes a nickname when you try to send to the GTS something with a censored nickname (warning: link contains potentially offensive words). You may want to use something censored, and the game will automatically change it into species name when sending it using GTS.