I’ve just copied over 11.000 files to a new Dokany container, totalling ~1 GB. Performance was VERY GOOD. The difference for practical purposes to normal work was negligible.
However my problem is that I plan to use Cryptomator as intended by its authors, that is to keep only private files on it and sync with untrusted cloud using cloud storage provider’s software (e.g. Google Drive). I’m not trying to protect my entire computer using Cryptomator. For that I have BitLocker (on one computer) or VeraCrypt (the second one).
Cryptomator (as far as I understand it) is NOT meant to install programs on it or keep database files on it or other data that requires very I/O intensive access. It’s a secure storage for private documents that are to be synchronized to cloud providers (or other destinations) that we don’t trust. I’ve managed to generate 20 GB of such documents during last 10 years (notarial documents, financial details, agreements with customers, court documents and sentences, and all kinds of scanned official papers that may be important someday, and so on). The rest of my 2 TB stuff doesn’t require high security with backup to cloud, and is rarely updated, so I back it up in a different way (to my NAS). But YMMV.