The "stabilized azimuth line" on the periscope was indeed used for speed estimation.
http://www.tvre.org/en/stabilized-azimuth-line
Of course SH3 doesn't have this, but as the boat keeps an unrealistic very steady course the basic periscope markings can do the job provided you don't move the periscope and steer straight.
The site linked above gives you a lot more information than you would ever want about historical procedures! Someone put a LOT of effort in!