I put together an Omaha beach landing mission too and had same result. One thing that seemed to help was making landing craft static objects instead of "ships" although that's a sacrifice some might not want to make. The focus of my mission is to take out 4 naval guns as well as 88's guarding nearby airbases. Along with that I have multiple randomly spawning groups of tanks heading from beach to airbases and removing all of them is only thing that gets rid of the one second stutter. Frustrating since a Normandy beach invasion doesn't work without troops invading. For now I'm going to keep mission as is and hope some optimizing can fix it.
I do agree that ships, static or not, and artillery as well are 2 things that cause this one second stutter with OK FPS problem the most.