Welcome to the forums! That's a really good question, actually.
And the answer is that you should feel free to destroy them at any time, and it's always worthwhile to do so if you are able to get to them. There is a certain AI Progress Floor below which the AI Progress will never go at any given time. If you hover over the AI Progress display at the top of the screen (in the latest betas, anyway) it will break it down for you.
So there are definitely times when destroying a data center will be "useless" in the short term, meaning that it will not cause the effective AI Progress to go down because of the AIP Floor. But, in all cases it remembers how much your total reduction is, and so that "useless" reduction will kick in and become useful by preventing future increases from effecting the overall effective AIP overmuch.
The lowest AIP is generally something like 1 at the start, and that floor increases as your total underlying AIP increases over the course of the game. So, no negative AIP ever.