No, magazines are military systems.
You've got a couple problems with this design. First of all, fuel harvesters and maintenance modules can't be used at the same time. Maintenance modules are only useful at a population, and you can't put a population on a gas giant. You'll need to split the fuel harvesting off into a second ship in a second fleet. Similarly, maintaining ships costs minerals. Not many, but some. You'll need some cargo space, and maybe some asteroid mining ships or something.
Really, though, if you're going to put this much effort into a military support city-ship, why not go all the way and have a whole orbital habitat so you can build maintenance supplies and missiles on-site? Actually, I suppose you could do the former with just automated mines and engineering brigades. Take forever to train them all, though.
By the way, is the tractor beam so this thing can tow its support bases? Be aware, a ship can only tow one other ship, no matter how many tractor beams it mounts. I believe, however, that if the support bases mount tractor beams, they can both clamp onto the mothership and it does pretty much the same thing.
Oh, and FYI you can mount CIWS on civilian vessels. So do it.