Seeing as Clip is common slang for Magazine when speaking of guns and in context. The Shadowrun writers may have chosen "Clip" on purpose. As to avoid confusion with people who's only knowledge of guns, is through RPGs.
Calling it a "Magazine" might conjure images of Toyfare or Newsweek or Wired, or Entertainment Weekly. Or.... Guns And Ammo. A clip in reference to a gun has fewer ways to be confused. Sure you can clip your gun to your belt but you can put your magazines in your belt as well but what if you have a magazine on guns and in the magazine there are clips or news clips about magazines?
lol
IRL It's nice to be clear and use proper terminology.
In a game. use what's fun and common.
If you want to use Magazine in your games. Use it.

It's not like it's a consistantly mis-spelled word. It's slang or a synonym through common parlance.
Lighten up!
Be excellent to each other!