i know in reality there actually is a bottom, but how do you hide the bottom with fog? Also, some bottomless pits are black, but I've seen some that have a faint blue glow coming from them. How do I make both effects?

I too want to know how to do this, I looked at Valve's env_fog with primary black and secondary dark blue, but it says nothing about how to get it to cover the bottom of a pit.

Use the env_fog_controller, measure the approximate distance to the "bottom" of your pit, and set the Fog Start value to about half of that distance. Make sure the Fog End value is at least 1000 higher than the Fog Start value. Use black as primary and secondary color, or some other colors of your choice. Cover the actual bottom of the pit with the tools/toolsblack_noportal texture. You can also add triggers like trigger_hurt and env_fade for a simple "falling to your death"-effect.
Experiment until you're satisfied.