but they could be to encourage breeders to breed even more.
Well first off, I think there's a flaw in that logic. A major one.
Well think about this. WHY would Gamefreak encourage you to breed more? It doesn't actually earn them any revenue. It doesn't advertise the game in any way. It does nothing beneficial for GameFreak at all - Why would they bother lieing to you, if all it does would be to potentially decrease their reputation, and has no benefits whatsoever.
Major Corporations run on the basis of increasing their profits by any means possible - preferably legal.
In that sense your idea that Gamefreak is lieing is completely off.
The mechanics behind the method were discovered by Smogon.
If you read Masuda's blog here
He specifically says 'rare colored Pokémon's Egg can be found little easier' - there is no actual mention of percentages, and the actual rate of increase.
Hackers are the one who have probably fond the actual rate of increase - which means that they have actually found the coding inside the games themselves relating to the Masuda Method.
ie. It's legit.
TLDR: Masuda Method has been proven, you've just been unlucky