Generally, if the vents (or perforations, or both) let in air, they also let in water. Less of a problem for short trips/light rain/fully-faired bike. More of a problem for longer trips/heavy rain/naked bike.
There are a few companies that have tried to get around this, with limited success.
Sidi makes a non-perforated boot (Vertigo) with a side air vent that you can close manually. (You can see it on the side of the right boot, below.) It comes in both regular and waterproof (Tepor) versions. It's probably hotter than the perfed version of the same boot, but at least, it's something.
Oxtar (now TCX), makes a touring boot that's supposedly both waterprooof and lets air through -- the Air Tech XCR. It uses a lot of fabric, with a breatheable waterproof membrane behind it. No idea how well it works, but it got a good write-up at newenough.com
For SoCal, however, I'd probably go with a perforated boot and suffer through the rare downpour. If you can afford two pair, supplement that with a waterproof touring boot for rainy days.