While I don't plan on hacking my Vue hardware anytime soon, I really like these topics.
In my mind's mind, I have designed an anny/vane that I think could work. All of this two-channel pulse business you are describing makes me think I'm not too far off.
I guess just a high density optical encoder is what I would use for the anny. Very low friction, no magnets, sealed unit. Just spins and makes pulses. For the vane, my mind's design uses a two-channel encoder of the same compact and sealed type, both channels have the same frequency, just offset and overlapping. We use them for speed/direction/acceleration monitoring of robotic arms in medical/OR equipment. They are about 25mm diameter and about 15mm thick. Four wires. The microscopic laser-cut screen/encoder is inside a sealed unit, directly around the shaft (actually a hole, that you pass (and grub-screw) a shaft through), with very low friction. To that, just add an adjustable pass-through opto-switch with a flag, so it knows where north is, and how many pulses (and phase/direction) from there to know which way the wind is blowing. It re-calibrates itself every time it passes that point (provided the flag/sensor hasn't been moved relative to North).