Where do you live? (From the pics I'm going to crazily guess somewhere in the Northeast maybe, with winter temps not usually below the teens or single digits... but I am probably 100% wrong of course LOL)
Also, how much wind is the shed exposed to from the front?
Ducks can take pretty much any sort of temperature, you're just trying to keep them out of predators' tummies and maybe somewhat wind-protected during the worst storms. And they are terribly messy
So honestly I'd suggest doing something much more radical than you would for chickens... maybe leave the little window open all year, and convert the top half of the door to all-mesh. That *might* be enough for ducks. If that seems likely to allow too much wind and weather to blow in, you could make the top half of the opposite wall all-mesh (in between the wall studs anyhow). I suppose it wouldn't hurt to have some means of temporarily covering those vents in a bad storm but on the whole, remember they're DUCKS
(FOr chickens, I'd say instead that you might want to convert the entirety of the two triangular top portions of the gable ends into vents, and possibly also add some high vents on at least one of the walls. But chickens are less messy and more weather-sensitive than ducks)
To cut holes in the wood, the simplest/safest solution would be to use a drill with large-diameter bit to make a starter hole in one or all of the corners of the desired shape, then use a power jigsaw (or sawzall, if you've made the starter holes big enough) to 'connect the dots' and remove the section of wood. Be attentive not to saw through studs or other wall structure
There are other ways of doing ti too, like with a circular saw or even a router, but I would recommend the starter-hole-and-jigsaw approach as safer.
Good luck, have fun,
Pat