You might as well just have a list system, and when you put the weapons in, you choose the weapons direction, without having to drag and drop things into slots.
Presumably dragging and dropping onto visible slots is a more enjoyable, understandable and fun process than using a series of drop lists...
If there were weapons/equipment that took up more than 1x1 slot, then there is strategy in placement, ie you cannot fit everything easily.
I think we need to justify the annoyance to players, and computational complexity for AI, of such a system better than just declaring that it exists. It isn't so much strategy as it is a potentially frustrating geometry or logic puzzle.
In this grid system a component would not take up 500 space or 100 space. It would take up 1x1 space or 2x3 space. This usage of space stuff would just be translated into a visual rather than number based system.
If we had only 1 slot per part, then that would be the size of each part. There would be no additional space requirement. All parts would take 1 slot. Why is it necessary or beneficial to make things more complicated than that? (not a rhetorical question)
Graphically, if we do (as i hope) build 3D models of the weaponry, and place them on the 3D hull models, it would be rather cool to have weaponry that's much bigger than the weapons you can build at the start. The dramatic impact of a death star with lots of little weapons isn't nearly as dramatic the one huge beam.
If we assume that one slot represents a fixed volume of physical space, then this might be a problem, but the number of slots in a hull doesn't necessarily have to scale proportionally with the on-screen apparent volume of a ship model, as long as we can fit the weapon models onto the hull model somehow... So, we could have a single-slot death-star laser that looks much bigger on the model than a single-slot pea shooter tier-1 PD weapon.
Tactically, 4 small Weapon Xs might do less total damage than a 4-slot single, large Weapon X, but would have a higher chance of doing some damage (4 chances), and/or be able to simultaneously target multiple enemies. So small weapons might be better at PD or any small fast targets, while big weapons would have a natural advantage against large, slow or otherwise easy-to-hit targets. This mechanic seems pretty intuitive.
I suspect we'll want to have have separate types of weapon parts to do PD, SR, LR, or deal with fighters on a ship. So, the comparison between a single-slot and a four-slot version of the same weapon for PD vs. SR might not even be an askable question...