Yup. I just tested it in-game. BC performance against Thor remains awesome throughout the upgrade path. At full upgrades (+3/+3), a BC takes down a Thor losing slightly over 100 hp. Against 2 Thors at the same time, a BC kills both losing 300 hp. This is without Yamato cannon. With Yamato cannon, a BC can probably kill 3 Thors at the same time.

Thors are ridiculously powerful against Light air, especially when stacked, but against BCs, an armored unit with 3 starting armor, they simply fail.