So I've been doing some reading on how to work the hint brush and how to manage portals recently and thought I would give it a shot in a simple few rooms... this is what I've got so far.
The caulk hull with the hint brushes selected:
Loaded the .prt file:
It dosnt look to bad, I think...? There is however a weird group of portals just to the right of the camera. In each room/hall there is also another portal about 16 units high off the floor, you can see here:
In that last picture it looks like your floor is 16 units below zero on the z-axis. If this is the case then the extra portals there are being caused by cuts from the blocksize. (IIRC Q3map2 cuts blocks along Z as well as X/Y) The same goes for the top-down shot with the extra lines of portals along the -1024x line, and along 0y. View Show Blocks.
You can either work with the blocks, disable them by adding a _blocksize 0 0 0 worldspawn key, or not worry about a few extra cuts.
Currently I would recommend option 1 or 3 because overall I don't know if you've 'got' what hint brushes do at all. Hints can only add extra cuts and create more portals on top of the ones you get from structural geometry. They don't define leaves which looks like it might be how you're treating them. I can't see any portals in this map that look much like they wouldn't have been created by the existing structural geometry? I think you'll find you get almost the same portals if you compile without those hints.
Might be a good idea to link us to what you've read so far.
The point of hinting is to optimize the portals in such a way that it limits the PVS, thereby hiding geometry that the player can't really see.
In your map, if the player is standing in the bottom left corner of the room on the bottom (XY-view), you can trace a line through every portal. So essentially, every single room is still drawn at that location and you haven't achieved any performance benefits.
btw try 45 degree angled hints at corridor right angle turns rather than hints perpendicular to the geometry. not only do perpendicular hints give you nothing the structural geometry doesn't already give you, but it leaves more hints visible from any given spot, hence more leaves drawn
like so
edit: yes, i know the geometry would cut B in the right hand corridor into 3 leaves but they're small leaves and would still block vis to any room beyond C
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