is it just the file contents that get hashed? Is there any way to include the file name and or metadata such as creation date into the hashing process?
MD5 tools will generally work with the binary content of the file. But you are of course free to put the file name and modification time into the content that gets hashed as well. E.g.
(stat -c %Y filename; echo filename; cat filename) | md5sum
Of course to verify the hash sum you have to use the exact same procedure, or else your hash sums will differ (e.g. when using different date formats).
In general, all the file hashers encrypts only the binary content of the file.
You can prove this with the following process: