So, there ia 4X in space, the player controls 100-200 planets (with hands off approach, most decisions are made on a global level not per individual planets, for obvious reasons :)).

I was thinking of a pollution mechanic and I'm not sure how to approach it. Typically you would be building factories or something industry related which would generate pollution and then you would see how much industry would start to generate pollution and then have to make a decision to either accept pollution, limit indisutry or invest in ecology. With hands off approach (where you don't build factories directly) it would not make any sense.

How to make some sort of pollution mechanic but without making decisions on a per planet basis?

Since your game is following a hands-off approach, your game pollution mechanic does not have to be too complicated.  You should just implement an overall, or average air quality level and once passed, the game allows the player to make a general decision.  You don't necessarily have to make it complicated and the end result (giving the player an additional challenge) will still be achieved.

Could pollution be approached as just one more threat that an empire faces? Only instead of the intensity of the threat being from outside empires or loyalty of generals, it comes from the development actions that a player takes.

I suppose pollution might affect a planet's happiness, food production, or possibly other stats. As industrial production increases additional resources must be spent on ecology to mitigate negative impacts on other planetary values. Effectiveness of investment in ecology possibly affected by technological discoveries. As such, it can become just another input for resources allocated.

Unless you sync the pollution levels across entire clusters of planets, pollution mechanics are likely too fine of a detail for your game.

The biggest issue is the pollution is distributed on a per planet basis but the player reacts to it on a global level.

All right, let's start with a simple model to kickstart the discussion.

Each planet heals -1 pollution per turn and each factory produces +0.1 pollution per turn (capped at max 3 pollution per 10 factories, so the pollution does not grow infinitely on a planet). Each 1 pollution decreases output of all industries by -5% and population growth by -10%. Then the player can invest in technologies like "Additional 1 pollution is removed per turn" or "Each factory produces +0.05 pollution per turn instead of +0.1".

How about pollution as an "overdrive" mecahnic: A planet can handle pollution fine with normally working industry, but then you are allowed to "boost" the production at the cost of extra pollution. Not for individual planets, but maybe systems or all of them at once. Then, after the boost period, you can take care of the extra pollution by lowering the production or investing in cleanup or some other way. 

Basically, have a "turbo button" for your producation when you need it, and have pollution be a cooldown/recharge period for it. It's a common game mechanic, and it can be done globally with no micromanagement.