Heres some clarification. Basically, say its zero visibility and its foggy, or even low clouds, pilots can't see anything except for like when they are a hundred feet in the air, there is a system called the instrument landing system, which is a series of antennae that transmit the location of the runway and the angle of approach the plane should be taking. This is under instrument flight rules. (Theres visual flight rules when its nice weather, pilots can see what they're doing so they don't need guidance). Often it just means theres this gauge on the pilot's display that they have to keep centered and they will make it to the runway, but some planes can process the info themselves and let the autopilot take care of it. ILS requires good clearance since there is a lot of trust in the instruments and nothing really to check it, so smooth approaches are favored, which is why runway 9 (west approach) can have ILS, but runway 27, obviously the runway of choice (its almost always how Lindbergh runs) has too steep of an approach for ILS since there are so many obstructions among other reasons, so it kills the capacity when the weather is bad since the wind almost always comes from the west, and the hills are too steep in the east to really make Santa Anas felt on runway 9.
Also about the height limit, I dont know all the regulations for San Diego, but there is this imaginary ceiling that surrounds all runways that buildings cant go above obviously. The slope of it gets steeper the farther away you are, and I think Downtown is clear of 500', but the fact that planes can't really turn north in an emergency because of mission hills, they have to loop and do whatever over the bay, and downtown is sort of surrounded by the loop that the plane has to do to realign. Now this has less basis in fact than just an educated guess but I'm thinking thats why.
My airport design class came in handy haha. There actually was a group assigned to pretend they were solving the San Diego airport problem (I got Portland). You don't want to know what they had in mind.
For more info...
http://en.wikipedia.org/wiki/Instrument_landing_system