In passwords, yes. In filenames, theoretically yes but in practise problems seem to occur depending on the setup.
Correct. You can not “remove” this metadata. Cryptomator is made for the cloud and the cloud sync tools need those timestamps in order to know what to sync. If you want to encrypt stuff for local use, rather use Veracrypt or similar tools, that will hide those metadata.
See this post.
If any bit of a file flips, the file is can no longer be decrypted (but it won’t affect other files in the vault). There are checksums in various places (and they are required to prevent accidental decryption of tampered ciphertexts - which would allow some attacks). However, it is possible to recover the file as a whole or at least parts of the file depending on the position of the damaged byte. For the exact probabilities, see this post.