I'm usually a 4e guy but I'm finding it harder and harder to get a game of that going, so I'm now hopping back to 5e but finding a lot of things difficult with the Matrix... One such difficulty is Matrix Perception... Or more specifically, the question you get to ask of "Is any Icon running silent within 100 meters of me or on the host I'm on?"
What prevents a Matrix Spider from just constantly saying "I want to spend each Combat Turn doing Matrix Perception tests and always devoting 1 hit to asking if any silent running icons are around?" I mean sure there suppose to be doing other things too, but it feels like it counters Matrix stealthiness too hard from Deckers being able to lurk around or wait, since someone is always gonna ask that question if their running Host security.
Note that Hosts have an event horizon. So if you're penetrating some corp facility, the spider inside the host can't scan for your silent running icons unless you get inside the host with him. But, if the site has someone doing matrix overwatch OUTSIDE the host... yeah. Note that hosts do not have physical locations, and so the spider defending the host for a site does not need to be IN that site... he can telecommute to work from literally anywhere in the world. However if a person wants to be scanning the local airwaves for silent running icons physically inside a building, that person must be physically there.
Running silent is paradoxically a good way to announce "hey, there's an intrusion going on!". Basically, it's an analogue for what happens when you try to use invisibility to get by an astrally projecting mage or spirit

Are there anyways to counteract this or work around it?
Do some homework and find out if the site already uses silent running devices (like drones, or whatnot). if the site already has stuff running silent, then they won't be prone to checking for silent running icons, because they know they're gonna get back a hit on that. OTOH if the site insists all employees and devices keep everything on the up and up, then running silent is just gonna risk giving the game away.
The concept carries over to hacking: Once you have a mark on the host, you're temporarily a legit user in the eyes of the host/IC. You don't NEED to be running silent while hacking a host... indeed running silent can just end up putting the host on alert if Patrol IC checks say, once every minute to see if silent running icons are present...