I don't think changing how vents/capacitors work at this stage is worthwhile (for reasons Alex mentioned).
Leaving a bunch of mounts empty, perhaps all but a few, feels unintuitive to me but I can't deny there are some examples where this seems to be the optimal choice. Astrals and Drovers being cited, 2x Plasma Cannon Odyssey, 2x Plasma Cannon Paragon with minor PD, etc. This has historical precedence: HMS Dreadnought and the "All Big Gun" philosophy that was a paradigm shift for battleships. If the minor guns don't contribute to the primary role of the ship, why bother with them? All players are doing are coming to the same realization that warship designers had over one hundred years ago.
I don't think you can prevent that kind of specialization but here's why it's "bad" for gameplay to me: the only ships in the game that utilize this tactic are player-made. Enemy fleets and the Autofit algorithm try to fill every weapon mount. A new player might wise up eventually to leaving a few mounts empty but the vast majority of use-cases he/she will see initially are fully-armed ships. It will take a lot experimentation or going onto forums like this one for someone to think outside-the-box like that. There are a few tips at start up that say "having more guns is not necessarily better" but until someone sees the actual advantage in action, it doesn't really click. Instead, trying to work within-the-box, players will do what we've always done and use smaller weapons, max vents, use higher-efficiency weapons, etc., but still try to fill as many weapon mounts as possible. Leaving slots empty will not "feel" right because the game seems to be pushing you to fill them.
That's why I like an idea that was floated earlier in this thread and that is putting "something else" in a weapon mount. There's a ton of things you could do here, but what strikes me as very interesting is putting hullmod-like bonuses in empty weapon mounts is that if an extra auxiliary engine, some kind of local shield, extra missiles, etc. were physically on the ship, they could be disabled/destroyed mid-battle. Such a system reminds me of Homeworld 2 where the Capital ship Subsystems that allowed for building ships, hyperspace jumps, etc. were physical entities that could be targeted. But, perhaps the buffs/bonuses that these "mounted" hullmods have couldn't be achieved through traditional hullmods.
The point being, leaving slots empty would be an opportunity cost beyond just vents, OP, and flux efficiency. It could still work but it might not be intra-competitive against putting some kind of mounted hullmod on that does "X" and has a greater net effect on battles than flux efficiency. Where this goes wrong is that targeting individual weapon mounts is hard, not just for players, but for the AI and it would make EMP weapons extremely disruptive. But, it adds a wrinkle to battles and to ship design.