You've jus rediscovered what was widely discussed many times here - optimal speed of a boat.
FOr VIIB type it's 8.25 knots (and 8.5 knots after GW Kapselgeblase engine upgrade), for other types the speeds are different, individual (about 6 knots for type IIB, almost 9 for IXB and so on). Unless in rush or in need I always travel at optimal speed to save fuel. 8.25 Knots is decent enough for cruising in my opinion.
I really doubt there is a real difference between "surfaced" and "0 m" depth, as surfaced allready means that the boat has as much positive bouyancy as possible, and setting depth to 0 m will not add anything. But I might be wrong, especially if there are some game engine issues I don't know about. SH3 behaves strange in some situations.