I’ve been having the same problem since December as in the OP. It seemed to get a little better with various versions of Nvidia drivers, but the problem with Hearthstone has never been resolved. I even tried Nvidia’s “MPO Disable” Registry script (it had no effect).
I just tested setting the “High DPI” settings for the Hearthstone.exe file to “System (Enhanced)”, and that seems to have resolved the problem based on some basic testing. (I got the tip thanks to the thread at Hearthstone Hand Flickering since Patch - #14 by Groover-1696)
This is definitely something that Blizzard needs to fix ASAP. The problem has been easily reproducible for ~3 months, and there are thousands of views to these problem reports. It’s really frustrating to see something that should be really simple to fix ignored for so long.