Currently, arc lint --everything when using git will execute git ls-files -z to get a complete list of paths to lint. However, this won't include directories (either empty or not), since git just tracks files.
The result, is that linters will never be asked to lint directories even if they return true on shouldLintDirectories (ie: ArcanistFilenameLinter).
AFAIK, there is no straight forward way to do this on git, since it doesn't track directories. It seems that we may need to manually generate folder paths base on the actual file paths to actually get the expected results.