I wouldn't compromise the structural soundness of the roof because of the tiny amount of ventilation you'd get in those little gaps. Coops need way more ventilation than that, especially if you live in a hot, humid climate. Those gaps won't make much of a difference. But they support the corrugation of the panels and will extend the life of the roof. Plan on adding lots of actual ventilation (large open areas protected by hardware cloth) and don't worry about the closure strip spaces.
If you use closure strips to secure both ends of each panel, the middle will probably be fine just being drilled into the purlins. But I'm not a pro so can't say for sure if that's a good or a bad idea. The closure strips are easy to cut, so, just to be safe, you can cut a small section to insert and drill through where the panels attach to the purlins. They are not expensive either, so won't add too much to the total cost of the roof. Each strip is about a dollar (they come in packs of 6).