I play World of Warcraft from time to time, and I got this idea from the armor set options there. In your Ship menu, a selector setting that says "Config A, Config B" etc. What it does is that it saves your current ship configuration to that button. You can set up two configurations to begin with, with extra ones available to unlock with the completion of a mission. Tool-tipping over it will tell you how much damage you're going to incur by using it (like disabling an induvidual ship item does). It can highlight in red if it can't be activated due to module damage or lack of storage space. It would also list what modules need to be repaired before you can use it, or how much storage you need to free up.

... well, people dont really change the configure of their ship except on scanning blitzes and leveling. i personally would not use this option, because i have all the modules i would want equiped. except for the many NPC loots i have stocked up in my inventory. but thats an issue of decks...