If you are making a backup of a crypt by copying the underlying encrypted data, then rclone check will work just fine and it will check the checksums. This appears to be what you are doing.
If you copy the same file to two crypt remotes then the hashes will be different as the file is different each time it is encrypted, even if the keys, etc are the same.
Let's say you have two underlying remotes called A and B and the crypt versions cryptA and cryptB.
If your backup does rclone sync A: B: then rclone check A: B: will be an excellent check, checking the checksums.
If your backup does rclone sync cryptA: cryptB then rclone check cryptA: cryptB: will not check checksums. You could use rclone cryptcheck in this case, but note that it will involve downloading the data from one side and since in your case A and B are remote then is undesirable.
Looking through the thread I think you are doing rclone sync A: B: and your rclone check A: B: seems to be checking hashes just fine.