Here's the result of my testing, so far...
My hose from the skimmer to the pump has several joints (don't ask!), so I bought some putty that hardens like steel and sealed all those seams. Then, I ran the pump with the skimmer lid on and vacuum hose attached. I rubbed shaving cream over all the seams and confirmed (as best I can) that no air is getting in from the skimmer to the pump.
Then, I watched the pump basket for about 10 minutes. Definitely less air in there than before, so I conclude there WERE leaks, previously, in my hose from the skimmer to the pump.
Then, I watched the skimmer basket. As time went on, the water level slowly dropped, leaving more and more air in the skimmer. The skimmer lid (which is only kept on by suction) was letting SOMETHING through the edges, and it looked like air might have been mixed in with the stream. But, it was fully covered with water, and there was no "whirlpool", so I don't know if there really was air, or if there was, where it was coming from (maybe extracted from the water, itself?).
Anyway, I've given up on the whole vacuum thing. My pool was badly designed with such small holes. I think the problems began when I replaced my pump. I must have replaced it with a more powerful one, and the higher suction is causing too much vacuum when sucking through that small hole.
Instead of vacuuming (and instead of the aquabug auto vacuum), I'm going to get an Aquabot Rover Jr. It has it's own filter system, so I don't need to use the vacuum part of my pool.