Did they feel the motion when they were submerged?

Perhaps, but it quickly became much quieter. Down at 100 to 150 feet, the wave motion from the typical swells was mostly or completely gone. The boat was much steadier. However, they probably would be aware of up and down angles during larger changes in depth. Those were due to the operation of the boat and are separate from wave action.

Shortly after leaving port, the captain would usually do “angles and dangles.” This was normally announced in advance. The captain then ordered depth changes with larger up and down angles. This was done to shake loose any equipment and supplies that weren’t stored properly. It provided an opportunity to properly store everything before it could become a problem.