The RPM indicators are definitely in the command room. If you switch to the CE by right-clicking him, you can easily view them to the right of all the other main dials. I read tips on here soon after I got started with SH3 about avoiding escorts by keeping your RPM to <50, but had no idea how to find the RPM. Later I noticed the RPM gauges and was able to better judge the speed to set on the knotmeter.
The depth gauge probably relates to the Atlas Echolot - if you are in the navigator's position (again, right-click him in the command room to jump the camera to his spot) and ask for depth - you will see a little white arrow marker move around on the device, stopping when the reply 'ping' is heard. There is a circular gauge with markings - the depth can be read off that depending where the arrow stops (should you not want to read the reply from the NA in the text box!).
So it seems to have the same functionality as RB describes above - the depth is only shown when the depth is asked for, and not updated in real time. So probably this gauge controls the arrow. Still, I hope there are some other useful things to be found, or that I'm wrong!
