Unfortunately, there is no documentation but here is some info on these two problems:
EmptyEncryptedFile
It means that a 0 byte cleartext file (88 byte ciphertext file since the header is 88 bytes long) has been found. It doesn’t really have to mean anything because it’s totally valid to encrypt an empty cleartext file. That’s why it’s just informative.
OrphanMFile
It means that a file inside the directory m was found that doesn’t have a corresponding file in the directory d. m files are metadata files that are created for name shortening. If a filename is too long, such file will be created. Since Cryptomator doesn’t delete any m files even though they’re not needed anymore, you’ll get this information. These files cause no harm.