My coop isn't big enough for me to sit in, but I will sit just outside it sometimes and grab a duck that walks past

The best way I've found is to do it during the day with a big bag of meal worms. I will sit down, and while offering small handfuls of worms, I will grab each duck one at a time, and give it a good look over. I put her down, and grab another. They love these treats enough to put up with the intrusion. Even if you only do this once a week, you will be doing some good.
Grab the duck and feel it's crop and keel. Look into her eyes and nose, making sure they are clear. Move down the chest and feel the tummy and hips. Turn her over and examine her feet and legs. It takes about 20 seconds per duck, and the flock barely has time to notice.