He is worshipped as a god, as such this could quite well be the reason why he is not there, as either he has left for some reason, like he had important other business before Ganondorf actually attacked the Zora's and thus without his protection Ganondorf was able to attack them or with the triforce of power Jabu jabu knew he was no match for the power of one of the golden godesses. Anyone ever thought that maybe Jabu jabu is the wind fish from Link's awakening where your on the dream island?
The other option which is a very simple one, is that Ganondorf killed him, as I doubt nothing else would have been able to, though another question about Jabu (Sorry if this goes off topic slightly) is that Ganon had obviously gone inside of jabu to put that creature in him, so did he also use a fish to enter? or did his dark magic simply create the creature and didn't need to enter Jabu and that creature is what stops Jabu from eating.