I don't have any experience with the clear ridge caps, but the roof panels are going to be a problem long before the rest of the roof in my past experience.  I have had two different sheds with the side panels and I like them and haven't had any problems.  My current shed is probably 10 years old, and the panels don't show any signs of degrading like they seem to when put on the roof.  I will say that the material they use in these now is probably better than what the original panels were when somebody first had this bright idea.  As far as the birds, if you don't leave the doors open, I don't see why they would be a problem.  My shed has panels, but there isn't any place for a bird to get in, although occasionally when I leave the doors open all day in the summer and close them after dark, I'll have a bird or two in there in the morning.  My father in law had roof panels on his shed and we had to replace one this summer, so we just put steel in it's place.  Later on, he had the whole roof painted and they painted over the other panels.  His shed is really dark now, but there are large gaps under the doors and the birds can get in and out.  You can't go in there for anything without turning a light on, but the birds don't seem to mind being in the dark.

Mike