My most heavily modified, intimidating looking and personalized guns aren't for running, they're for carrying during civilian life. My characters invariably live in really bad neighborhoods, so they need some protection.
There are two kinds of gear. Disposables and personal gear. It's the same concept with vehicles, weapons, almost anything. Sometimes you want a generic stolen car you can blow up at the scene when you are done, or a cheap gun you can throw in a dumpster. They may not be as effective as the top-of-the-line modded equipment that some Runners carry, but it is less traceable, and that is what matters.
On the other hand, the Rigger's tricked-out personalized uber-van, the Sniper's chameleon coated Barrett, the Hacker's 6/6/6/6 Commlink or the Adept's Weapon Focus katana, is not going to be discarded. If it has to be left behind, it could be an entire Run just to get it back (or find a replacement).