Hi! I am a new guy!
Unfortunately, Thunderstone is the only evolutionary stone that is unavailable at the Stone Emporium. Sorry. :(
There is are four evolutionary stones available in the game, they are in Routes 10, 11, 13 and 18.
Hope I helped. :)
Source and Source
It's because the only evolutionary stones you can get in the Stone Emporium are the Fire, Water and Leaf Stones.
If you want a Thunderstone click here to see all the way you can get a Thunderstone in Pokémon X and Y.
You can get a Thunderstone on Route 10 and Route 11 in Pokémon X and Y. For help getting each Thunderstone click on this video for the Thunderstone on Route 10 and this video for the Thunderstone on Route 11.
Hope I helped :)