During an attack, the position of the sub relative to the nav map doesn't matter. The navigator would plot the sub course as a straight line and plot the target position relative to the straight line course of the sub.
Hitman has a plotter tool for SH4 that I pictured. We need one for SH3. hint hint.... The sub would be set at a certain speed. Say 5 knots, then every 3 or 5 minute time slot, the position of the target would be plotted. The hash markes would show the subs position after each time increment with the numbers representing the subs speed. So actually position of the sub as far as long/lat wasn't a factor in plotting an intercept.