The 9.9 there is like a 100 pound kid standing out on the end of that port tube.
The half log is like a big bobber under the boat right in the center bow.
That boat looks like it is floating exactly right to me.
The one thing I'd check on that boat is to put it on the trailer and give it a good shake to see if there is any water in any tube.
Without the added 9.9 weight and with the maximum motor allowed I would bet that is a nice performing boat. I also don't think removing the center log will make you any happier with the ride or performance of the boat. You would probably accomplish more by removing the big motor and moving the 9.9 to the transom. I have to assume you use the big motor on different bodies of water though.
As to the pressure in logs, that is a completely moot point. I have been in, on, under and all around dozens of pontoon boats in the last 30 years. I have never seen one without vents in the logs to equalize pressure inside the log and out. It keeps the tubes from popping on warm days and collapsing on cool nights. If you think you don't have them, look at where the tube meets the M bracket at the top, I bet you will find something there that vents the tube in at least one place.