Whew! So much to say, so little to go on. First...you need an architect. Hire one. Then you need an engineer. Hire one of them too. Hiring a contractor to consult on cost and practical issues is a good thing too. Once your team is assembled, listen...hard! Best of luck!

Love the armless sofa-bench! Try using it in the center as a "cross-linking" piece between the sofa and chairs. That way people can sit on both sides of it, conversing with the sofa people and the chair people. Put the chairs where it is and use the side table from the left of the pic, or the one with flowers, between them. You'll need one huge rug to anchor the space or two smaller, and very similar ones, to put on either side of the blue sofa-bench. The other two side tables are too tall and too short for your seating pieces, so ditch them. Use your coffee table between the sofa and armless sofa (18" away from each of them.) Here's a chart for judging table and lamp heights as you'll need to work on that for balance. Please try this arrangement, and post by commenting and using the Attach Images button to add pix of the update. We'll tweak it on out from there.

How do you decorate your place, what kind of style, colors, and feelings? That will greatly influence the type of door you might want. Also, think of your budget, and whether you want to install it yourself or hire a professional (you don't need to tell us, just keep that in mind). Then look around Houzz, in the products page, they have lots of interior sliding doors and hinged ones, from elegant frosted glass in a dark wood frame, to rustic reclaimed wood planks. You may not want to purchase that exact model, but it might give you a better idea of what would fulfill your airflow needs without sacrificing style.

The amazing thing is that you have the luxury of approaching the architect about these issues. Laminated glass should address the security along with any alarm or security system you plan on installing, though the laminated glass may have size limitations. Regarding the waterproofing you should contact the architect, contactor and waterproofing subcontractor, or see about hiring an independent waterproofing specialist who can detail and warranty the condition. As a design consideration, make the lower area a garden or gallery or sculpture area and upper should be all glass. Maybe a garden roof there too if accessible or visible. In any case looks like an amazing place!!