That's why I've changed from a vacuum line to the air intake for putting the HHO into the motor. I live in the mountains a coast a lot, so the generator saw lots of max. vacuum time. It's necessary to leave some air space in the top of the generator which creates more problems with a significant vacuum "volume" that is very powerful. My generator was completely sealed with no leaks and the problems were numerous.
The biggest problem with the vacuum line hookup is the lower boiling point of water at a vacuum. A running temperature of 160 or 170F becomes boiling at a certain vacuum level. So "thermal runaway" can occur under a vacuum when it wouldn't if hooked up to the air intake.
The vacuum effect in the bubbler was an issue I couldn't overcome. Water would get sucked out no matter what I did. The advantages of hooking up to a vacuum line are far outweighed by the disadvantages, IMO.
With my HHO input going to the air intake, I have no loss of water out of the bubbler and no problem leaving an adequate air space in the generator. The car actually seems to run better with the current hookup, too.