I used to go to a club layout, and after wacking my head more than a couple times, some quite painful that put me on the floor, I began wearing a plastic hard hat. The kids thought it was funny, and it did look odd, but my head appreciated the protection.
Under my house I have a couple water pipes that I've run into more than a few times, again with a lot of pain. I've since put pipe insulation on them to pad the impact, until I can reroute the pipes.
Similarly where you have the duck-unders I recommend padding them w foam rubber to pad the inevitable collision. Also any place where you know you will lean in w your head, put a layer of foam rubber.
Identify the duck-under. As you are looking at the floor when you go under, so paint the floor to identify the location of the duck-under. Then paint a radius extending maybe 3 feet from the duck-under, so you know when you can straighten up and know that you are clear of the duck-under.
Gary