"...material [like wood] rot, rodents/insects, mold..."
All of the above. I do repair and replacement of residential structures, and all of these issues arise from excessive humidity/moisture. That's basically what keeps my rent paid.
Regarding animals as part of a gardening system, they're basically essential as producers of the inputs necessary for photosynthetic plants, from CO2 to other waste products animals create that are food for plants. You don't have to yourself eat them, but can market them to folks that do. However, I note that most people undertaking vegetarian diets do so for reasons other than nutritional, even if they rationalize them that way, so selling animals may be objectionable for you.
The point of aquaponics is that it doesn't take more room than that necessary to grow plants already does, and enables the provision of the necessary inputs plants require in a natural way that doesn't require purchasing those nutrients. Animals are generally the highest quality nutrition potential to people, so including them in farming tends to dramatically improve the nutrition available to farmers, particularly in subsistence conditions. I've seen very large aquaponics systems using thousands of gallons of tanks in a 3 bedroom apartment, for example.
You seem very capable of analyzing the light, and other, requirements of your garden, and alone can detail your specific purposes, needs, and what you are comfortable with. All I could hope to do is perhaps suggest things you hadn't thought of, which I think I did, and hope it has been to your benefit.