Are there any objectively real gaps? Not just gaps in what we know or can demonstrate, but scientifically perceivable, natural effects that truly do not have natural causes?
Well, creation ex nihilo certainly involves supernatural causes and natural effects. But I tend to doubt God's initial act of creation is a scientifically perceivable cause (if only because there's no "before" against which to measure the change from non-being to being), and I'm not at all sanguine there will turn out to be any other acts of creation any more perceivable to science.
By faith, we know that God immediately creates each human soul, but try getting an NSF grant to study that. And the other gaps, in cosmology and evolutionary biology and so forth?
Obviously, no one knows what there is to know about what we don't know about. But I see two trends that suggest our current gaps in knowledge do not include any real gaps in natural causes.
First, the more dramatic but less telling trend that our gaps in knowledge are constantly shrinking. It's dramatic because of the effects it has had on people who made confident but false assumptions about the way things are based on everyday observation or a literal reading of Scripture. It's not as telling a trend and some would have it, though, since it is also the trend predicted by the hypothesis that some of our gaps in knowledge do contain real gaps in natural causes.
The second trend is harder to define. I'll call it what we've learned about the way things work -- which, in a word, is "very well indeed." There is an elegance to nature that all can recognize, even those who do not recognize the intelligence that created it. When materialistic scientists say there is "no need for God" in whatever mechanism they're studying, we should consider that a compliment. After all, there's no need for a watchmaker inside a well-made watch; the fact that it works without the watchmaker constantly tinkering with it is what we mean when we say it's "well-made." As created by God, you might say, Nature comes well stocked with natural causes.
These two trends suggest two things to me: First, don't bet on any particular gap in knowledge to contain a gap in natural causes. Second, God generally seems to work through natural causes, so he may well always work through them.