I can't recall ever running an SOHC4 with the dipstick removed. You'd think in 30 years of ownership, I'd have tried that at least once.
Anyway, the backside of the pistons face the crankcase and they are going to move air when going up and down.
I think I would check your breather system to see if there is any blockage. On the Cb550 there is a foam filter that can clog up with water and oil. I'm not sure how or if the Cb650 is different. But, the breather hose and what not is going to offer more airflow resistance than the big open hole for the dipstick. It will breathe wherever there is the least resistance.
Oh, and you're not SUPPOSED to run the engine with the dipstick out, you know. Anyway, it's not a normal run mode, for sure.
Cheers,