When I had my old RH battleship, the Enterprise, i had to use a cruiser in order to buy weapons for it.
I had the enterprise parked all the time at her assigned system, and every time i needed guns I had to use my cruiser in order to get the guns from a far away location. Mostly to avoid having to move such huge ship through a lot of asteroid fields... Now it is no longer possible to do that unfortunately.
If the docking system cannot be modified, then:
certain planets (namely, those where large ships can't dock) will have to have their death zones reduced in diameter.
Or, we create a equipment buying ship. Said ship would have one mount of each type and level. That will allow it to buy any weapon in order to carry it to the ship its intended to use. A moderate cargo space, so it can carry a number of unmounted stuff, and not enough energy to shot said weapons. A moderated shield, and an awful lot of bots / batts which could allow said ship to be used as a supply ship for fleets.
I prefer option one. Much easier to implement and will cause no unbalance.
(If you find any mistake in my English, please let me know via a PM)
(Really, I speak terrible English, so please, tell me if I make mistakes. I'd like to improve it a bit )