By then the area will be relatively empty but as long as you exercise standard urban common sense (cross the street if you feel uncomfortable, stay out of dark alleys, and don't wake sleeping transients) you'll be fine. The route you provided adds an unnecessary five blocks to the walk however. From Pier 39:
- Walk west along the Embarcadero,
- About a half block west of Pier 39 the Embacadero will split -- take the main, LEFT branch, Jefferson, rather than continuing on the Embarcadero and heading towards the water, Franciscan Crab Restaurant, etc.
- Continue heading west on Jefferson two blocks until Taylor Street (look for the big Fisherman's Wharf Crab and Wheel sign),
- Turn LEFT (south) on Taylor
- Head two blocks south along Taylor to North Point.
- Turn RIGHT onto North Point. Your hotel will be half a block down the street.