(how short do brushes have to be to not work anymore?)
Brushes wear down until they stop making good contact with the armature.
Sometimes because of spring travel or length, other times the wire that is attached to the brush bottoms out keeping the brush from moving further down in the brush holder so it can no longer contact the armature which I suspect is the cause of your failure based on the images you posted.
Another question that came to mind from this was, what actually can go wrong in the housing where those magnets are?, it is kind of the last place that I would suspect.
Not much. Usually it's just magnets bonded to the case, so unless you dropped it or otherwise damaged them they should be fine.
Is spring placement an indicator? I could compare the two.
Not always which is why I would want to open up the pump to confirm.
If you look at image 3 if the shaft rotated clockwise the armature rotates with the springs pulling them down.
If it ran counter clockwise it would be pushing the brushes into the springs.
This leads me to believe that rotation should be clockwise, but this is not guaranteed since I have rebuilt golf cart generator/starter motors with the exact same brush spring setup that can reversed by changing a couple of leads around causing the brushes to push out against the springs.
From what you are saying, Does this mean it would be a counterclockwise motor?
Well in the past CW and CCW were labled different depending on the manufacturer and application.
Modern motors at least the AC ones I deal with more often have moved to more of a standard naming system to avoid confusion CW lead end or CCW shaft end, etc. but I'm not sure if DC motors are doing this yet so it's hard to say.
Back to my guess...
Looking at the back of the motor (brush end) at my nose I think it should be spinning clockwise.
Flipping it over and holding the shaft end at my nose it would be spinning counter clockwise.
Again this is just speculation AKA your milage may very.