I wouldn't think most people would be running silent. The world is setup to run open to get the most out of your devices, so only the ultra-paranoid or those expecting bad stuff to happen would be running silent.
I would start your world off with most people running open and if you find the players are having a field day hacking things to pieces and really disrupting everything, then you can shift to more people running silent. I think you will find it will not be that big of a deal and the hacker will still have tons of other things to worry about than seemingly everyone in the world running silent.
And even if everyone does run silent, it would be in the decker's best interest to do some advance scouting and marking before getting into combat. Remember, 100m is a pretty decent range, so most teams will be able to wait a few combat turns to let the decker set things up and get some marks on devices he finds. If the decker is always getting stuck trying to mark things once combat starts, then you might want to suggest changing party tactics to give the decker at least 15-30 seconds (which even in AR is going to be at least 5-10 complex actions, probably twice that).