It probably won't be possible to fit this into Endless Space 2 but maybe something to consider for Endless Space 3.

It is always frustrating to see ships with low health but still able to do everything and then in a second they just explode.

That is the drawback of a "health" system.

What I love is what was introduced in "War Thunder".

You don't have health but components and armour. A bullet either penetrates and causes damage to a component or bounces off.
The fact that you are shooting 20 times at the same sport has no extra effect.

Of course is space you have shields and lasers to add to that but those aren't difficult obstacles.

It would be great if battles (specially since they are so cinematic oriented) would include such a system. 

You would also have ships with damages engines that need to be repaired after battle or abandoned and thing would get a lot more interesting.

In the GD documnet about battles, it is said that weapons and defense module can be disabled on their own during the battles. After the battle result however, the whole damage is averaged as a single health bar. I don't know if there will be any specific weapons tactics focusing on this kind of damage, however.

But this will still be "health bar" thinking instead of small gun's being unable to do any damage to big armor.

The whole idea would need to have some assumption on how shields work.

Are they solids that any projectile needs to penetrate (just like armor). 

Or is this some anti laser contraption that ships / bullets can fly trough.

If we assume shields are a solid then things get simple.

I would see it as something like this if we assume that shields are mostly anti laser and objects can fly trough them.

Shields vs. Canons -> small reduction of damage (bullets get slowed down a little)

Shields vs. Rockets -> no reduction (they just fly past it and continue to the target

Shields vs. Lasers -> big reduction 

Armour vs. Canons -> depends on cannon and armour. You either get penetration and damage something or you don't.

Armour vs. Rockets -> depends on rockets and armour. You either get penetration and damage something or you don't. The difference between cannons is that rockets have a lot more punch.

Armour vs. Lasers -> depends on laser and armour. You either get penetration and damage something or you don't. Lasers focus on a small area and should be able to penetrate better than cannons.

Defence cannons vs. Canons -> has no effect

Defence cannons vs. Rockets -> if they hit the rocket then full reduction of damage. Can be used as small offensive cannons also.

Defence cannons vs. Lasers -> has no effect