I don't think that stopping a ship from current speed to zero is necessarily unrealistic - besides, 0 is a nice number with which to do this kind of simple modelling using vectors... zero allows you to factor out "final velocity" from equations of motion.

that would make your 'knowns' as follows:
Code:

u: "initial velocity" (m/s) = ships max. speed
v: "final velocity" (m/s) = 0 - ship isn't moving anywhere (maybe the anchor is down?)
a: "acceleration" ( (m/s)/s ) = a negative value - how fast your ship is decelerating

as someone already said, you can find the time it takes to stop with rearranged to then displacement can be calculated with legend:
Code:

s: "displacement" (m) t: "time" (s)
u: "initial velocity" (m/s) v: "final velocity" (m/s)
a: "acceleration" ( (m/s)/s )

I don't know what you mean by "Proper speed to its destination" if a ship is decelerating, then its velocity is constantly changing.