Depends. I have a pump that I can control the rate to each outlet. With no adjustment I would assume, that all else being equal on the lines, the flow would be the same only to the used ones, provided you plug the unused ones.
I also have one that manually adjusts the flow of each. But I also just bought a Hagen Elite 802 that has no adjustment. However, the specs list the flow as "1500 x 2 cc/minute" while the 801 (with one output) lists the flow as "2500 cc/minute". So I think in the case of the 802, you get 1500 out of each no matter what you do to each, but I suppose it's possible that blocking the outflow of one may result in increased flow out the other (and probably end up damaging the unit).
There are different types of multi output air pumps. I'm going to use pump mechanism to mean one diaphram setup and one vibratory pumping arm.
A TetraTec Deep water pump uses four pump mechanisms and two air outlets. Some pumps have two mechanisms and two outlets. So, the answer to your question about those dual outlet pumps is yes, they can have different outputs, but shouldn't as the parts are assembled pretty precisely these days.
Larger linear pumps quite often come with a manifold with several barbs for air lines, but use only one pump mechanism.
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