Membrane pumps basically consist of a membrane, something to agitate it, and a pair of one-way valves. Turning the valves around also flips the direction of air flowing through the pump, turning a normal air pump into a vacuum pump.
What can we expect from such a thing? Aquariums are usually less than a meter high, so a pump made for pumping air down to the bottom of such a thing should be able to provide a suitable pressure difference (about 10000 Pa, or 0.1 bar) just to get an idea about the magnitude.
Turning it into a vacuum pump shouldn't change that significantly. Compared to a professional ("real") vacuum pump that doesn't sound like a lot (they go down to almost 1 bar pressure difference), but it's enough to be very useful.
It turns out that the only thing to do was to rotate one part by 180 degrees.