Yes, the air is pulled out AS LONG AS YOU DON'T LOSE THE CONNECTION OVER THE BLEEDER SCREW! As I said before, there is not a positive connection of the vacuum pump on the screw.
There is a BIG difference in FLUSHING brakes and BLEEDING brakes. In the case of flushing, IF YOU'RE CAREFUL and don't lose the connection you can GET BY with the vacuum. If the system has been open and there is considerable air in the system you will find that unless you are using a high volume, motorized vacuum pump, you won't be able to pull enough volume with a vacuum method to keep the air out of the upper components (ABS.)
With a handheld vacuum pump, you pull a little vacuum with a stroke and it will pull down a little fluid, but a bubble can and probably will rise in the system while you are gripping for the next pump of the vac pump handle.
If you are using a pressure bleeder or the two man method, you are getting enough volume to push fluid on through, getting air out.
When it comes down to it, the issue is adequate fluid volume which you can't get with a hand pumped bleeder.