OK first off all fuel tanks are vented. otherwise as you burned fuel you would suck a vacuum in the tank as you burned fuel. Think about it. Way back when the tank was directly vented, now it goes through a charcoal canister, which BTW does not remove any moisture.
As far as excess condensation from low fuel causing problems, I gotta tell you that in over 30 years in this business I have never heard of a genuine case, just FOAF stories. Now in the interest of full disclosure, I live in LA which is not the humidity capitol of the know western world.
As far as vapor lock goes, it is not as much a thing of the past as you might think. If you have a fuel injected car that has the main pressure pump external to the fuel tank, and a helper pump in the tank you can have vapor lock if the helper pump fails. I haven’t seen two pump system in about 12 years or so, but there are fuel injected cars on the road that have them.
Where is the fuel pump pickup? One of two places. Either flat on the bottom of the tank, or flat on the bottom of a small canister that is flat on the bottom of the tank. The purpose of the canister (about the size of a coffee can open at the top) is to hold a supply of fuel for when the level is low and the fuel sloshes. This also allows the car to start when the fuel level is low, and you park on a grade where the fuel runs over to a corner.
The fuel cooling the pump. yes it does, but it is cooled by the fuel flowing through it, it does not need fuel around it. As long as fuel is flowing trough it, the pump is being cooled. If the fuel flow stops, the engine stops, the pump stops, so no danger of overheating of the pump.
Now if you run the tank so low that the engine is misfiring, and just barely chugging along you are doing damage to the car. Misfire is bad, very very bad. Misfire destroys catalytic converters in very short order. If you run your car to that point you might wind up killing the converter trying to get to the next gas station.
If on the other hand you get gas before you get to this point, I can see no problems, and I have never seen an authoritative cite to the contrary.
Rhubarb If I was working on your car I would look for either a leak above the in tank pump (inside the tank of course) or pump that was not flat against the bottom of the tank, or a plugged fuel filter. In the interest of cost change the fuel filter first.