That's not hacking, that's more cheating using a device. Technically hacking, but doesn't permanently change data in a fashion, instead manipulating it via an external client.
Nintendo DO NOT WANT hackers doing things at all. I though the anti piracy things they did such as the no EXP in newer Pokemon games would have made that obvious. They do not want people getting the ROMs at all, they just want to create a game that people will enjoy. Also less people will hack a "blank" game that has no elements of the original ROM as you need to add a hell of a lot of stuff into it (including the battle system, by the way), and Game Freak are more obsessed with making their own games than allowing them to be modified. It's not a good business plan to do what you are suggesting. It's also not going to prevent the spread of the ROM, as the original ROM can still be used by pirates, so there is little need to do it. Nearly any ROM can be found by pirates as they are leaked from Game Freak by accident or by one person on purpose and then put on the internet (like the Black and White ROMs), so either way, the piracy continues, it can't really be stopped.