Nope, sorry, that's just how it is in Sub Command
Doesn't make any sense to me, either. You'll also notice, if you haven't already, that if you order a course change, your ship instantly starts changing course at the rate of change it'll take through the whole turn. What I mean by that is there's no increase or decrease in the rate of change through the turn which would happen from the rudder moving from 0 to whatever angle it has to be and then coming back to 0 again.
If you don't want these problems, yes, get Dangerous Waters. There are much more advanced ship dynamics in that. If you start a turn at 15 knots and reduce speed to 5 knots, you will overshoot the turn because of the large amount of momentum. Speed up and slow down is a lot slower, but the slow down still isn't as slow as I'd like. The ship will actually roll, too, unlike in Sub Command.
Tom Clancy SSN actually has some real good ship dynamics, in my opinion, but that's a very arcade-like game. You can actually employ "sprint and drift" effectively. Slow down takes a while in that game, and it seems water drag is modeled at least proportional to accurate drag. By that, I mean that you lose speed more quickly at higher speeds because the force of drag is proportional to the square of velocity. At lower speeds, it can take forever to lose speed.