So your setup would be velcro on pouch, then velcro to velcro with the second velcro being held to pants via magnets so the sandwitch would look like this: leather,cloth,velcro,velcro,magnet,pant,magnet, leg.
Fixing the magent to the velcro will be slightly tricky. If you don't sew the magnet to the pant leg it will shift. If your pants arn't lined your leg will rub on the magnets could be uncomfortable. Beyond that it should work but it adds several layers of potential fail points and I'd worry about its longevity.
Your tricorder should be ok with magnets while not is use. Infact the GMProps uses a reed magnet to trigger the racket sound. I myself am in the process of upgrading to the GMProps tricorder. There are other tricorders that employ the use of a SIM card which could get interfered with as could a cell phone and various magnetic strips on credit cards. Your Trek stuff should be ok, its primarly the mundane extra stuff you might be carrying.
A question I would ask is when do you see yourself not wearing the pouch? I always bring along my props as part of the costume and having a hands free way of carrying them is a must.
On a side track, did you have many issues getting your GMProps electronics inside your tricorder body?And which body did you end up using?