Well real uboats did have stadimeters, and they did actually use mast height to estimate range, and had books that indicated mast height for common ships. Experienced captains though probably guesstimated mast height or range, and even speed. Also certain ships tend to go at certain speeds on given situations.
I'm guessing since you are using 3:15 trick, that you are familiar with Wazoo's manual targeting guide.
http://www.subsim.com/radioroom/showthread.php?t=206381 That trick is more a game trick then one in reality per say, though they may have have used the same sort of trick based on the measuring instruments they used for charting
I think in reality they would measure it on the chart and then compare the time and distance to a book that had pre-calculated estimates. That way you would not have to do complex calculations or be required to count to a certain time between observations.
Ultimately though they did do a lot of targeting calculations by plotting. Plotting is even still done today in modern submarines, but with computers and software to help.
Back then you really did only have a handful of ways to figure out speed. Guessing from experience, hydrophones, radar, or the stadimeter. With experience you can manually set up shots on the fly though, and in the early part of the war uboats would often just charge in under the cover of night, fire a spread, and submerge, hoping one of the fish would hit.