The important part here is when it is encrypted. When you archive it as .zip or .tar.gz and then encrypt it, you can’t read any information about what’s the file is except for the name of the file, and as you’re saying, the file size of the encrypted file archive. You can’t see into the archive if the archive is encrypted and you can’t tell what is in the archived file once it is encrypted. You just see that there is one file. I haven’t used Cryptomator but if “Upload to Cryptomator” means that you’re encrypting in, then uploading the encrypted file, both methods you’re describing will pad the resulting archive in a way that it isn’t possible to see what’s there without breaking the encryption, and it will make the archived file slightly bigger than it would have been.
I believe even the filenames are encrypted, so matching up file sizes becomes one way for an attacker to pinpoint a target (thus OP’s question if I’m understanding.)
Cryptomator has a Community Forum where the devs May be able to answer your questions directly.
I haven’t used it to know if it behaves the way I suggested it does. I assume it does, however I recommend asking on the cryptomator community if you can’t find it in the documentation. Links to both in posts in this thread which I don’t know how to link to explicitly.