I am really sorry about the trouble. You will need about 9MB for each minute of video. So you do need to make sure you have ample disk space.
The key thing here is that Moodle manages the activity(quiz, activity, forum etc) and by extension the files associated with that activity. So to remove files, you need to remove the attempts or submissions or posts that contain them. Moodle then deletes the files or moves them to trash. The actual restoration of file space (true deletion of file) takes about 4 days for some reason.
If a file is no longer necessary then presumably neither is the activity/post/submission containing it. So that really is the best way to manage the files. Poodll could do better in reporting about files, I agree. But its just not a good idea for Poodll to try to remove files that are contained in activities.
I know that you are using assignments and students have relatively short enrolment periods. Since Moodle does not offer the ability to delete assignment submissions individually, my suggestion for pruning files is to have two courses and alternate them. When one course no longer has users enroled, then reset the course. This will remove the files associated. You can be specific and reset only the assignments in the course if that is better.