Yeah. I got the same problem: the drive-icon has disappeared in MacOS Big Sur. It reappears after you've clicked on it but disappears again after a while. Pretty annoying.
I've also tried replacing the icon with the one in the Boxcryptor.app resources folder but the effect is the same.
Looks like a bug to me!
Ref: Boxcryptor 2.37.1043 on MacOS 11.0.1