Like any other real or virtual drive, Cryptomator vaults don’t delete file you choose to delete and don’t send them to your Trash folder, but create a local .Trash folder. I’ve never had issues deleting these from external drives as needed. Since that folder had become 100GB, I deleted the one in the unlocked vault folder as well. What happened was the vault got corrupt, Cryptomator threw many warnings on how it can’t access it and threw me out of the vault and the vault is not accessible and usable anymore.
This can’t be the normal behavior. I can’t afford to have gigabytes of junk data that I’m not allowed to clear manually.