On one of my coops I have a large plexiglass picture window, it has been wonderful. The birds will sit in front of it looking out all the time, they actually fight for a prime seat, lol. The sun coming in wakes them up every morning.
On a second smaller coop, it is a dog house converted into a chicken house, I put windows in each door but this time I used LEXAN. At first I thought it was the same as plexiglass but found it to be much thicker than p-glass and a couple dollars more. I like the LEXAN much better.
As far as the regular screen goes, I dont think you will keep flies out with it. Flies will still come in through the door and lay eggs, then you will have tons of flies TRAPPED in there that cannot find their way out. I have seen this happen before!! Also screen will not prevent preditors, you will need to use hardware cloth for protection.
Back to your original question...YES!! That is a good idea as a vent or window cover. If you are only doing this for cold weather, why not just use hardware cloth for the window and vent openings and when it gets cold, go to
Walmart and purchase a clear heavy duty shower curtain. They are very thick, thicker than any plastic you will find, you can get either 5 mil thick or 12 mil thick, and they are CRYSTAL CLEAR!! This is what I use all winter and it keeps the weather out and still allows me to see in and them to see out. This would offer just as much protection from the weather as plexiglass but is much easier to use, easier to store, and much less expensive and still look nice.
OK, sorry, I'm done now, LOL. Good luck.