It's not that simple. The acceleration is faster in any gear but not at any speed. At speeds in which the shorter final drive forces you into a higher gear, the acceleration is actually slower than with the stock final drive. So what you are doing is making the car faster at some speeds, and slower at others. Thus it might help your lap times at some tracks, where you spend a lot of time at speeds where it helps, and it might hurt your lap times at others, where you spend a lot of time at speeds where it hurts.

Read through the links for more details, particularly this post which tells the actual speed ranges where it helps and hurts.