(I don't watch pro Dota games yet so don't take my word on this too literally.)
I think the reason pro players wouldn't use Sniper much is because he's pretty much just good at taking down someone 1v1. If you are more people, and if you manage to ambush him or disable him, he's toast. I know this goes for most people (fuck, the stuns in Dota can be really brutal. Screw you Chaos Knight), but Sniper the most squishy bastard IN THE GAME.
He does good damage, his Headshot thing is crazy and he has long range, but I imagine pro players would counter/ambush him pretty easily.