I just had a farmer buddy walk into my office so I showed it to him. All I did was show him the picture and said “What are these little sliding doors for?” Without hesitating he said “They’re for letting the birds in, the birds eat the flies.”
Take that for what it’s worth. I know, you said they have joists in them, but that’s why I just showed him the picture and left our discussion out of it. As soon as I saw the picture, he’s the person I wanted to ask. Now, his farm is for produce as opposed to livestock (he doesn’t have horses/cows/poultry as far as I know), but he’s the only person I see on a regular basis that owns a farm and would have the most knowledge of something like this.
people do things to prevent birds from coming into barns. i’ve seen vents baffled so birds can’t go in and out easily.
i expect lots of architectural features will be time, heritage, location and use dependent.
Fungi can prosper only where it’s moist. So if the roof is sound, interior beams are not vulnerable.