I tend not to like the "God of the gaps" idea. That is, I don't think "Here's a thing science can't explain, so it must be that Goddidit." I'm more likely to think "Hm, interesting", and keep my theology separate from my science.
I suspect there will always be questions that science just can't quite answer, but I don't think of this as an "excuse" to believe in God, just... a sign that humans are neither perfect nor all-knowing.
I think in 1000 years (barring some massive setback, eg a nuclear war sending us back to the stone age), science will have reached the point where few if any religious people are using "Well, here's a thing science can't explain, so Goddidit, take that, atheists" as an argument. Instead, I think religion will, increasingly, become a deeply personal thing, and concern itself more with a. how to live a good life, and b. what happens afterwards, than about the literal truth of any given holy text or whatever. And what faith you are, or aren't, will pretty much not matter to anyone except *maybe* your prospective mate, or someone who wants to go to church (or temple or synagogue or circle or whatever) with you.