Are not Box launchers supposed to be harder to reload?
If cargo loading can be used what prevents me from just building a separate magazine ship and reload from it in deep space without any need for hangars?
This. Box launchers are supposed to be harder to reload. Also, box launchers NEED to be harder to reload, for balance reason. If not, the already overwhelming advantage of box launchers at starting tech level will get even higher.
With the fact that early in the game box launchers can almost completely ignore point defense, there is little reason to build any other weapon system tactically. Sure, you need a strong economy to feed box launchers. But tactically, box launcher ships are always better. You just need to bring enough of them and you can destroy the opponent without any possible defense on his part.
If box launchers were reloaded like cargo, it would be insane. The major disadvantage of box launchers would disappear. Then it would be truly unbalanced.
In case it was not apparent, I am in favor of option 2). You want a box launcher large warship? Make an hangar that can contain said ship.
EDIT:
And better explain before the "but it is realistic that box launchers are easy to reload" argument gets whipped out. This is a game. So it NEEDS balance, or else there's no point.
Want to have your perfectly realistic box launchers that reload in no time? Fine, give me infinite range railguns, as it should be, then we can talk about it. Once I can use my railguns to target your planet from the other side of the system, AS IT SHOULD BE, then you can have your perfectly realistic box launchers.
The bottom line is, in a game there need to be compromises so that the game is actually fun to play. If you remove all the limitations and make a weapon system OVERWHELMINGLY more useful than any other, what's the point of playing?