They certainly have to with VGC being as big as it is. There's also the fact that their servers are always collecting data and they use that data to craft the next games. Aside from Doubles & 3v3, they still see that "Free Battles" are very much 6v6 Battles and I would go so far as to tell you that they know the gist of our tiers as well. When they look at all that data showing Politoed being used more than Kyorge or Arceus, you'd better believe that they look for a reason. Whether or not they know of Smogon's existence, they certainly know there's a force in place that restricts those Uber Pokemon so they may be balancing as such. Also, I'm completely convinced Game Freak has someone that at least keeps tabs on Smogon just by the fact that Honedge not only exists, but it was given its own reveal trailer. The fabled Steel/Ghost-mon EXISTS, folks! Not quite Kitsunoh, but good enough! 3D battles, a hard nerf to Dragons & Fighting-types, a Steel/Ghost-type, AND they still haven't released Shadow Tag Chandy, I mean it must be the Year of Jirachi because all of our collective wishes are coming true.