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I have this issue for some time now, but I think it is becoming more apparent as time gets by.
When the engine is cold and I run a downhill and i develop some speed without actually pressing the gas pedal after some minutes of moving like that, when I want to accelerate with the throttle the engine stalls for a while and I have to rev it in neutral so as to make it run smoothly. I used to think that this has to do with exhaust fumes returning back due to not pressing the throttle? The last few months it starts to annoy me. Could this be a dying O2 sensor? It has more than 100K on, and I notice a slaggish feel when I am between 1 to 8 percent of throttle.

Once I had the same issue.
I changed the spark plugs and the problem gone.
Other reason can be the faulty/damaged/filthy IACV.

Why this is happening only when accelerating on downhill with closed throttle?

This is quite complicated after some research we did. If you remember the story, if you want to swap a 4-1 header to our d14s you need to change the o2 too, and put a heated one. Due to its relocation the stock sensor looses its right temperature when the gases for some reason become cooler resulting in stallings. I have a heated 02 sensor installed, with 3 wires, (1 extra for the earthing, the other for the signal and the third for the power to heat it. The only bad side of this is that this lambda cannot be connected with the 3 wires directly to the car as the ecu doesn't have a command for heating the sensor whenever it is needed. So the heating works all the time all these years and it might not work as it should. So when I downhill with the throttle closed the gases lose temperature and this results in some stalling. Fortunately it doesn't happen often.

The lambda is a resistive heater if I put the term correctly. What I try to say: the hotter it gets, the more it resists current trough it, thereby limiting it's heat build-up. So it should be pretty safe.

But indeed it seems like the manifold gets clogged by something. Could it be filthy injectors making a rich puddle in the manifold when airflow is really low (as in downhilling with almost engine braking)?

Check valves for clearance and do a compression test to see if all 4 cylinders are still operating the same. Small differences are exagerated when in very low loads I like to think.