I’ve just answered the first part about empty folders in a feature request on GitHub: Issue #991
Regarding the second part: Currently, the only way to safely remove metadata files (*.lng files inside the m directory) is to use Sanitizer.
java -jar C:\path\to\sanitizer-0.16.jar check --vault C:\path\to\vault --solve OrphanMFile
Good news: Long filenames will be treated differently in the upcoming version 1.5.0 of Cryptomator. We’ll update our vault format and after that there won’t be an m directory anymore.