I've performed some testing on this newly found information.
stargateprovider wrote:You can actually get more systems than you usually could, so it's a nice code. It even gives you a warning when you are about to exceed the system cap, but lets you do it anyway.
Actually, the game only lets you exceed the cap if it is the only option. If there are other options to choose from, it will grey out the option to add the system. Exceeding the cap has to be forced onto the player.
Having multiple system options is not advised. Each one will cause warning text to appear, which quickly uses up space in the text box and forcing options out of it. A solution to this would be to add the systems further down the event chain so they won't clutter the same event.
Forcing the game to add a drone system when you already have it installed will delete the drones from the existing slots. I assume the same would happen to weapons.
edit: After some more testing, I've found that adding a system you already have places a duplicate system in that room. This is bad, because you can no longer repair the system without a repair bomb, since the duplicate is in the way.