I have often wondered about depth keeping also in regards to realism in SH3/GWX. There are some very detailed explanations of this in Edward Young's great book 'One of Our Submarines'.
http://www.amazon.co.uk/One-Submarin.../dp/1844151069
After reading those sections again I realize that this was not the Captains job. He would tell his officer in charge of this task if the sub was not at the proper depth, but he didn't actually do it himself. This is very well simulated in SH3/GWX. Your helmsman is doing his job very well. No need to yell at him.
Good hunting.