Hey Dave, welcome to the forum..
Interesting idea you propose. A while back I read Mike Oehler's book 'The Earth-Sheltered Solar Greenhouse' which inspired me too to one day build a solar passive greenhouse (above ground or walipini - havent yet decided) and also use it to house my chooks at night for heating etc.
A couple of thoughts to your questions:
1) It sounds like you are planning to build an inground pond with the chickens pooping into it, is this correct? If so, yes, excess ammonia in the form of chook poop entering the fish pond could become an issue if not well managed, or you have insufficient growbed filtration (chook poop will place a much higher load on your biofilter). Might also make the water murky. Apart from this, yes it CAN be done, and others have shown its possible with ducks, chooks etc (search this forum) but the main concern is the pathogen risk as you point out. But who knows.. I've been peeing into my AP system and throwing in the occasional worm tea and handful of compost (which contained rotted down meat, dead rats etc - I compost everything here) for over 2 years now and I'm still standing never been sick so take what you will from my advice hehe
2) I suspect, but cannot confirm, there is a natural biological/ecological protection barrier protecting the internal flesh of the plants from becoming contaminated with pathogens which in turn could be passed onto us - just think, before the industrial revolution and rise of petroleum-based fertilisers farmers for thousands of years have been fertilising their food crops with animal manure, blood and bone and urea. I think the bigger risk is the pathogens being present upon, and in turn ingested by us, on the EXTERIOR surfaces/leaves of the crops. Wash the vegies thoroughly before consumption and I reckon you'll be right
3) This point is subjective and will be influenced by a range of factors such as your location/climate and amount of sun hours hitting the greenhouse. If I were you, I'd build a greenhouse with adequate passive ventilation and cross flow. A lot of farmers where I live roll up the sides of their greenhouses over summertime, and let them down at night or on cold nights (and permantly down in winter), but this may not be practical to contain the chooks unless you had netting installed also to keep them in ?
Oil activated thermal opening greenhouse vents are also good and operate automatically without electricity
Consider digging a 'cold sink' in your greenhouse, where the coolest air will sink into and become trapped. Consider housing the animals in this trench to warm the coldest air. Checkout the book mentioned above for more on this and the image below:
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