Yes. Thats how cryptomator works. If you open your vault, a new drive is provided in which you copy the files you want to encrypt. Is the vault closed, there is obviously no vault-drive that could be found by 3rd party software.
No. Cryptomator is not a backup solution. If you want to have cryptomator encrypted backups, you’ll have to use backup software that backups into the vault. (here is s my recommendation)
The backup solution then detects what is known and untouched in your backup and whats not, and then do the backup.