I also own and use daily an Eheim Surface Extractor, great tool for the hobby, keep you're tank clean and there will be no problem with it clogging, I clean it at everywater change, because it does it's job, surface scum, so a weekly cleaning is good.
I too run topless tank and lose a bit of water a week, that is my topoff indicator
It will not lose it's prime unless water level drop's below water line within the unit.
I would suggest you build or buy a reactor, for more effective C02 desolution.

Some folk's say they are noisy, I dont have that problem

So...I have nothing but good thing's to say about the Extractor. But I am bias!