There are lights that are made to look directional, but I think in the end there is just a sphere light put where the spot light is pointing. Do I have that right?

There are light shaft objects that provide illumination over the entire length and width of the shaft.

Though there doesn't seem to be as many of these lighting effects in NV as there was in FO3

Yep, usually paired with the light beam FX Elanthil01 mentions.

Only omnidirectional emmitters. (like spheres or the 'light shafts' Elanthil mentions.)

I really hope the new TES:V engine has all the current lighting stuff. Lighing is undoubtably THE most important aspect of setting mood and making 'good' gamespaces.