Yes and no, I think you're right as far as why the velocity component exists in one of Karassik's equations, it's required for converting from a suction gauge reading - this is Bernoulli's Equation coming into play. Velocity head, however, is a finite portion of the net energy available in the pump suction region, hence Net Positive Suction Head.
Acceleration head, on the other hand, is actually another loss of energy from that which was available in the suction vessel, over and above the steady-state line losses calculated based on friction and fluid velocity. It's subtracted the same way you subtract line losses. The interesting thing is that it's additive, the head lost as you accelerate the liquid from a stop is recovered as the liquid decelerates, minus some frictional losses, so by installing a suction stabilizer of some sort, you can gain back almost all the energy 'lost', and nearly neutralize the effect entirely.
However, since NPSH calcs rely on the worst case condition, only the losses associated from accelerating the liquid is considered, and deducted from the steady state NPSHA prior to comparison with NPSHR.