Regarding your first question, a pitched roof can indeed provide more stability compared to a flat roof, especially if you're concerned about load-bearing capacity. However, it's also possible to strengthen a flat roof/deck by adding proper bracing and support beams. It might be worth discussing the specific design and engineering details with your dock builder to ensure it meets your needs.
As for your second question, for upper deck flooring, you might want to consider
Timber Joists. They can provide a sturdy and reliable foundation for your deck. Additionally, you can explore modern decking materials that are designed to be waterproof, non-slip, and comfortable to walk on, such as composite decking.