Hi Lorenzo!
Congratulations for your succesful Zynthian build 
A friend of mine and ZynAddSubFX lover too have been using one of my Zynthians with its wind-controller although we had to make some adjustments …
Regarding aftertouch, not all engines support it. Same for CC2, although this is easy to map to CC11 (expression) or CC7 (volume), which is supported by almost every engine. That is what we did for using my friend’s wind controller with ZynAddSubFX. We also had to put the “velocity sensibility” to the maximum.
Probably you also could map the after-touch messages to CC11 or CC7, but i never tried.
I think your experience will help to improve the Zynthian behaviour with this kind of controller. I will be very receptive to your proposals 
Kind Regards!