There is absolutely nothing wrong with encrypting files on a volume (hard disk) that is also encrypted. Encryption doesn't "distort" anything; it's a reversible mathematical transformation of the input data. The cipher neither knows nor cares whether the input data is already encrypted; there's no special flag saying "this data is encrypted already!" that might get somehow confused. It's all just data.
- File contents in plain text: A
- File gets encrypted using per-file encryption utility: ENCf(A) = B
- Encrypted file gets stored on an encrypted file system: ENCv(B) = C
- Encrypted file is read off of the encrypted file system (for example, to upload): DECv(C) = B
- Encrypted file is uploaded to a cloud service: upload(B)
- Encrypted file is download from a cloud service to an encrypted volume: ENCv(download(B)) = C
- Encrypted file is read off the disk and into the per-file decryption utility: DECf(DECv(C)) = DECf(B) = A.
("A", "B", and "C" are placeholder variables for the actual data, not literal values. "ENCf" and "DECf" are the per-file encrypt and decrypt functions, using the key you supply. "ENCv" and "DECv" are the volume-wide (VeraCrypt) encrypt and decrypt functions, using VeraCrypt's key for that volume.)
Now, it is important to not mess up the ordering (some ciphers will tolerate this, but some will not); DECf(C) != B, and DECv(DECf(C)) != A (probably). However, in practice this won't happen. You can't even tell where files begin and end on an encrypted volume unless you decrypt (some of) it first, so you aren't going to do something silly like try to decrypt C using cryptomator* and then try to decrypt the result of that using VeraCrypt. If you can even see the encrypted file is there, it's already passed through VeraCrypt so the data you see if you read it is B, not C, and you can safely pass it to cryptomator or whatever.
I've actually built, with a friend, a simple tool for doing this using the open-source
gpg program for the file-level encryption. It worked fine.
*I don't know cryptomator and am not specifically endorsing it.