This is largely true if you run a 'typical' D&D game that tops out in the 15th-18th level range. But as other posters have mentioned, there are several instances where deities fight each other and even kill each other. For events of such world-shaking importance, it is best for the DM to decide what kind of game he wants to run and let that decide what happens rather than trying to play out the overthrow of the titans with a ream of divine character sheets and fistfulls of dice.
Deities and Demigods makes it abundantly clear that the deities it presents are not omnipotent, not even Taiia from the example monotheistic faith. In essence they are just extremely powerful creatures in terms of their abilities and crunchy bits under the rules. As a practical matter, they may well be percieved as omnipotent, because who's really going to cast a gate spell and go spank a deity until it cries uncle?
Despite the fact that I've never used the statistics for deities, I like the fact that they are statted out and there are rules for making your own deities. We've all seen 1st-level characters, so we know where the bottom rung for power is in the typical campaign. Adding deities with stats sets the other end of that spectrum in a concrete way. As a DM, I dig the idea of being able to read over a creature knowing that it's one of the most powerful in the game and there's (usually) not much that the characters can do about it.