Okay first let me tell you that you can actually meet one or more of Game Freak's employees in the Pokémon Games. Although the part about the hidden door is only a rumour and is in fact not true.
Game Freak employees appear in each of the main series games, with their HQ being on the third floor of the Celadon Condominiums in Kanto. In the games in which Kanto is not visitable, they appear on vacation. With a group being in Lilycove City in Hoenn, staying in the Cove Lily Motel, and a single member staying at the Hotel Grand Lake in Valor Lakefront in Sinnoh. The main reason to visit them is to obtain a Diploma, awarded after the completion of the Pokédex. In Pokémon HeartGold and SoulSilver, the Sound Designer gives the player the GB Sounds after the player has obtained all 8 Kanto Badges.
Game Freak has another HQ in Unova being in a building in Castelia City. The Game Freak HQ is located in a large building on Castelia Street's right side. The building has only one accessible floor—22F—where the Game Freak Developers can be found.
In Pokémon Black and White, a character representing Shigeki Morimoto can be battled after stopping Team Plasma. In Black and White 2, aside from Morimoto, another employee which is based on Kouji Nishino can also be fought. Nishino uses a Snorlax as his highest level Pokémon, a reference to his nickname カビゴン Kabigon, after which Snorlax is named. In the English Versions, he calls himself Snorlax. Both Morimoto and Nishino have the Trainer class GAME FREAK.
Note: I am not aware if there is a Pokémon Creator you can talk to in Pokemon X and Y but there is a high chance that there will be. So if there is a Pokémon Creator that you can talk to that's located in a room that's accessible through a hidden door it will have to be on X and Y as there aren't any other creators you can talk to than the one's I mentioned in the other Pokémon Games.
Hope I helped :)