4X in space.

You lead the Terran empire (humans). There are civilized alien races (humanoids) and uncivilized aliens (non humanoids, considered unsentient). Civilized races consider other civilized as somewhat worthy of compassion (no genocide allowed, no bio/chemical weapons, etc). Uncivilized races outright eat other races population upon conquest :) Extermination of uncivilized aliens is encouraged by all means. Civilized races can be somewhat integrated into the Terran empire (but not as equals).

Now, I wonder how to model population (especially food and breeding of conquered races). Note that I prefer some simple mechanic since it's not the core of the game.

At this moment a planet can hold X population, when the limit is exceeded the population can still grow (possibly infinitely) but very slowly. Note that the player have no means of moving population between planets, they are local (upon conquest 10 units of Terran population is spawned).

When a planet is conquered by a civilized race other civilized races can live there as well (the conquered ones) but they slowly die over time (negative growth), they also ear no food, pay no taxes and take no space (too unrealistic and inintuitive, I don't like it). So basically when a planet is conquered only the new owner's race is really considered the population...

The reason I made it this way is because I don't want to make options for the player to manipulate/micromanage population (the game is simply not about it), and if I made civilized aliens count as ral population that eat and uses space it would require a player to have some options to exterminate them... which I don't like for many reasons :)

Still, I'm unhappy with my current model :)

At the very least civilized aliens should eat food and act as workers in the industrial facilities on the planet...

Still, I'm unhappy with my current model :)

I am also unhappy with your current model. I would like to address your question, but there are other more important problems that I just want to say something about. I apologize in advance that I did not address your question directly--i simply couldn't get around the other things I'm seeing. This IS intended to be helpful:

You are assuming too much. IT sounds like you want to control the behaviors of the aliens in a way that makes them conform to a particular morality. You are making them behave in predictable ways. It may seem sensible to you to say, "well, of course civilized races wouldn't do THAT to each other."

This sort of sensible thinking, however, severely limits the experience. I don't want all the civilized aliens to act in a nice, predictable manner. I want to discover that the cuddly bear people I thought were my friends just savagely raped my next-door alien neighbors. Put some spice in it! Your current model sounds very plain.

There should not be a nice, neat distinction between civilized and uncivilized races. Some of the uncivilized races should be sentient. This is 4x we're talking about. It absolutely MUST have fascinating, unique, and unexpected surprises awaiting potential explorers. We call it 4x, but really it's "eXploration, and the other 3 X's".

If there is no dark unknown to explore, then it is not 4x.

At the very least civilized aliens should eat food and act as workers in the industrial facilities on the planet...

Soo... make them do that ?

I don't see the problem, as long as they 're slowly dying(slave-labour) they won't give a too-strong boost to the conquering empire,

but developed colonies will have an easier time becoming/staying(?) developed after conquest.

Still, I'm unhappy with my current model

That's because you don't realy have a model, you just refused to (outright) kill hostile population and refused to (ab)use them as well.

Another option you might like is turning conquered civilized races into uncivilized races, they can adapt to the wilderness(adapt to other food/maxpop/growth etc.-stats) and hide there, then start a guerilla-war against the conquering population.