What are these files in MongoDB?
Those files belong to the journal, which is essentially what is going to guarantee consistency of your data as you write it to the database.  It is pre-allocated at 3GB (unless you start with --smallfiles) and will not be included in the size of your database.  This will not grow with your database but rather it will be based on how much you are writing to the database.  Unless you are doing a lot of writes the journal size will be 3GB.  If you are curious about journaling and how it works, there is a great write up here.

As for the database itself, the disk space usage question has been asked and answered many times - yes a regular compact (and repair or resync) can be needed, but it very much depends on what you are doing with the data.