As Sy goes to get into his car, he looks up and seems Emmit. He waves but Emmit just closes the curtains without so much as nod.
I know he was becoming suspicious about Sy, but their last conversation indicates that Emmit pushed that out of his mind and believed in his ‘friend’ once more.
It’s also shown throughout the season just how cruel and vindictive Emmit can be towards his ‘friend’. Treats him like a pet, more than a partner at times.
Did he ever truly trust him? Did he ever truly care about him in a regard like that?
The logical choice would be that Varga wouldn’t tell him his plans, as he always kept him in the dark. But that doesn’t explain the cold shoulder.