Mp4 is a container (for the audio and video) - the files inside the container have to be Roku-compatible, or it won't be able to read them. I assume that's the issue you're seeing.
Actually that is not true. If you stick an mp4 extension a text file the Roku Media Player will see it just fine. Of course it will not play.
When looking for files the Roku Media Player, and most other simple Roku players, just read the file names when looking for playable media. They do not check the format nor try to read the metadata.
More complex players, like Plex, do some reading of the media but I think even those will still provide a listing for improper files.
The problem the OP is seeing lies elsewhere. It is possible that something in the directory structure or file system is causing problems.
A listing of one file tree that is not detected and one that is would help us to help.
I had one case where an improperly formatted sub-directory caused one of the Roku players to stop reading at that point even though there was more on the disk.