I am sure we have all been in a situation where you join a match just to hear the last knell of the match start drums. The match is already started, and you have no idea what ship or team you are on, or what any of the loadouts are. The common practice in this situation is to 'abandon' the match to retool, then rejoin.
Other times, you simply find yourself outmatched because you happened to bring the wrong tools. That buff hammer seemed like a good idea at first. It worked so well in the last match, right? *OMGFIREEVERWHEREBOOM*. Nope. Once again, 'abandon' the match to retool, or suffer the same death over and over.
So, my suggestion is to make a physical toolbox somewhere on the ship. Players may change tools while remaining in the game and staying aware of the situation. As it is an actual physical object, crew will still need to take time to run to, open, and select new tools from the box. This would make it impractical to change tools during a heated battle, so I don't see that aspect changing much. It would, however, give crews a little time to reassess and adapt their loadouts during lulls.