I'll admit I find your idea intriguing, but it doesn't seem like it could fit my current concept very well.

In a "sandbox" game, it would fit (and would even bridge efficiently with my energy system) allowing any ship to become anything.

My concept revolves around hull types that are much more restrictive. I really want to build the lore/feel/gameplay around these specific hulls.

Each faction have few hulls which they can customize a bit, but not too much as to derail them from their original purpose: a science ship can't be turned into a missile frigate, etc.

Each of these hulls should contribute to the overall strengths and weaknesses of their faction and cover some of the basic roles (leave some opened) etc.

As a result, being able to field any amount of weapons on any ship would be too customizable, and though interesting as a system, it wouldn't support the current design I have in place.

To be in-line with my current approach, not only do I need to have specific slots in place, but ideally, these slots should not only be labeled as "weapon", but rather, as a class of weapon I can use in this slot (energy-powered weapons such as beams, for example, would only theoretically require an energy port, whereas missile launchers would require some form of "door" to the inner cargo rooms of the ship and only minimal power). Since each weapon type plays a much different role, I need to limit the amount of customization a player can make to the core craft's functionality without making it too hermetic...

Players can manually disable/enable specific components on their ships (shield generators, sensors, even engines!) which allows them to manage power shortage

Manually? That's excessive... Make it simplier, like insufficient energy reduces (not disables) beam weapons rate of fire, shields, combat speed (in equal proportions).

Having more energy allows you to sustain generator damage for sure, and makes you more versatile and mobile, but it is a limited advantage to not using the extra power you have onboard. If you would spent it on weapons or passive defenses instead, you wouldn't need to worry about getting damaged anyway...

A but lame idea: the ship enters combat with random status of the reactor (50%-100%), like if space travel could discharge the reactor temporarily and you can't predict but how much.

(I'm not a fan of this but it should work)

Note not necessarily reactor damage is needed to reduce power available, like power circuits, power lines in the hull, etc could be destroyed making loses in energy.

Another idea, beam weapons overheat the longer the combat lasts and require more power per shot each combat round OR reactor gradually lowers efficiency each combat round (overheated or something).

I feel that such a system would force players to design 'energetic ships' (those with shields and weapons) around a single beam weapon to maximize their lasting power, whereas other ships should maximize power output of their guns/missile launchers.

Maybe you are exaggerating? First the player would try to put a proper reactor to not have excessive energy in the first place. Second, if that's a problem you could simply make beam/shields designs less efficient/more expensive.

Also, do you really see a space ship that would not require energy to operate? Missile launchers should require some energy too, also all these targetting computers, ECMs, communication arrays, combat scanners, etc. In theory, I can see a scenario where a beam weapon ship uses not that much more power that one without these (I mean energy used mostly by non weapon components), althrough I agree it's a bit of stretching the energy rules

While I agree that micro-managing every component can be troublesome, I can see value in turning on/off a cloaking device for example. Also, I like the idea that components become less efficient as they take damage, but still consume the same amount of energy. In many cases, turning off a low-producing shield generator to revert all power to weapons or engines may be advisable. I'm trying to come up with something that sums it up more efficiently than a list of on/off switches (like some sort of Bridge Order) but it's proving a bit difficult.

Remember here that my actual game will generally won't allow you to control above 100 ships (and only in the late game!). I want each ship to feel unique, and I feel this is one way to achieve that (helping them with damage taken, etc.)

Having ship systems overheat as combat proceeds feels gimmicky at best, but it does serve a function. I wonder if it could be rationalized in a different way? Perhaps treating energy as a short-term finite resource would help (aka, every shot depletes from the energy pool, and the energy pool only refreshes once per game turn).

I'll tinker with this possibility and see whether it affects other mechanics negatively.

Re: ship design, the reactor is not actually chosen by the player, it comes as a stock component aboard a specific hull. The player has little control over the entire energy output of each hull design (unless they "sacrifice" their special components slots to add extra energy instead of valuable sub-systems).

Making beam weapons less efficient is already part of the plan: since they don't consume ordnance and pool from infinite reserves of energy, they need to be less efficient. My means of achieving this currently is to have damage that scales up over time, the longer they hit the same target.

In this given approach, this makes them drastically less efficient than guns and cannons at short range (which deliver full damage from the first second) and hardly compete with longer ranged missiles which deliver more damage (but can be intercepted). They do serve a purpose however as they can effectively intercept missiles or focus fire on larger threats and eventually get to higher damage outputs.

But it's a strong weapon to deal with, as it can effectively wreck balancing plans.

Other weapon systems do use energy, but much less. In fact, it isn't about how much energy you have dedicated to your beam weapons, but how much idle power you can reroute to recharge or cool down your actual beam weapons. Beam weapons are nothing but focused directed energy after all. I anticipate that while cooling down, they would leave the ship in a pretty tight spot (all excess energy has been unleashed and the ship is recharging from the reactor). Any hit on shields at that point could be decisive, so perhaps that is one way of balancing this out (shields power oscillating with energy reserves and becoming extremely weak when beams are done firing and need to cooldown).

Food for thought.