I found a bug (2.5 bugs),
* some "respawn event" let me choose a starting module, I choose "Homing", then when I visited the POI system, then I got a choice to select "Homing" again (I GOT to see what that would do), and the result was that nothing happened, I didn't get any upgrade that time (as expected).
* Same with "Ricochet" upgrade, but this time it was both times selected from the POI selection. It also shows up in the "Trade station" as a selectable option.
AHA! NOT a Bug?
The new modules does not "upgrade", they "replace".
So THAT is why you are allowed to buy multiple of the same thing, because it COULD be better than your current one.
IMPROVEMENT:
Some kind of color or other marking on eg. the item border, to show that it is better or worse than your current one, and if you do buy it, maybe add a pop-up warning, just to confirm that the player indeed intends to buy a worse item.