You and I are cut from the same cloth. I'm a GTD practitioner myself, although the particulars differ.
In my case, I have an inbox and then I have an action box, which is what I actually read. The action box collects all unread messages and any messages which I have marked as flagged. Flagged means that the message is something that should be in my universe, it will require an action from me or my attention. At any given time, I seem to have between 3 and 10 flagged messages, plus the unreads, but I am pretty vigilant about acting on things as soon as I can.
For me, anything else is just in the regular inbox, which I hardly ever look at. I suppose it is the equivalent of your vault. The search function on OS X mail is fast and robust enough with my 15,000 message vault that I quit filing things a long time ago. I realized I was simply scratching my own organizational itches without adding simplicity or value to my system.
My mail system runs itself -- I had to set up a couple of smart mailboxes, which took about 10 minutes. I run my life out of the excellent program
Omnifocus, which is a task manager that I use for hold/waiting, and other contexts. Since the mail is so easily searchable, I don't worry about creating more walls in that part of my life. As a bonus, my OF database automatically syncs to my iPhone, so I am working from the same lists at all times. Unfortunately, OF is OS X only. I hear that there are hacks to MS Outlook to add similar functionality.
I've been kicking around an idea about for a thread about this stuff.