@croydon - You really have to be very prepared if you're going to take kids to the zoo. Particularly if you're using public transport, but I would take a car if at all possible.
Food and drinks and things are expensive and not great quality (not San Diego particularly, just all zoos in general), so try to bring your own snacks and things. You also need sunblock, hats, jackets, and so forth.
That zoo, as you say, is not a half day event. The last time I was there I didn't manage to see the whole thing even though I was there from the opening hour. With kids it's even worse.
So, just don't plan to do, say Sea World and the Zoo on the same day, it's just not feasible.