Hi.
Cryptomator was designed for online files. It is not designed to fully encrypt your local system.
So if your local OS is creating thumbnails of files in your local vault, thats because for your OS the vault is just an other network location.
If you want to encrypt your local system completely, you should consider a solution designed for that.
(Soprry I would suggest one, but I am not very familiar with linux systems)
See here: Security Target — Cryptomator 1.7.0 documentation
or here: What does Cryptomator protect me against?