I've known a fair number of atheists and spent a lot of time in dialogue with atheists, and many of them take a very dim view of superstition just as I do. They often see the omens, astrology, routine prophecies of the end times, the wearing of charms, and so on as a misunderstanding of causality rooted in magical thinking and agency over-detection, just as I do.
Given that most of them are scientific realists, their general rejection of the supernatural (not just the supernatural causality of superstition) seems to provide them with a means of resisting the tug of magical thinking and agency over-detection more often than others on average. At the very least, they are more likely to explicitly reject certain kinds of magical thinking and agency over-detection, especially those associated with religion, pseudo-science, and various "paranormal" claims.
Though I'm deeply religious myself, I certainly see value in cultivating a resistance to superstition, including superstitious practices which inevitably tend to accrete around religions. Fortunately, having two parents educated in the hard sciences helped to form me in such a way that I have a well-internalized resistance to superstition of my own.
That said, I can certainly fall prey to magical thinking and agency over-detection at times. I notice it occasionally, and there are probably times when I don't notice it as well. That's largely because these are normal human cognitive traits, thought patterns into which we fall quite easily because they were useful for our survival in times of harsh survival pressure under which quick and dirty heuristics are better than lengthy and less inaccurate methodologies for arriving at correct conclusions.
Despite my intuitions, there is very good evidence that atheists aren't really any less prone to utilizing those quick and dirty heuristics (magical thinking and agency over-detection) than anyone else when the chips are down. Understandably, they are likely to resort to those heuristics under pressure just as anyone else is, their resistance to superstition decreasing the more dangerous it gets in the foxhole.
It makes sense that our risk-management instincts kick in under pressure, so I certainly don't think anyone needs to feel shame for that. Given the way we evolved and the instincts (quick and dirty as they are) propelling us to make decisions under pressure, we should expect ourselves to fall prey to magical thinking and agency over-detection because that's just what our brains do as naturally as they do anything else.
But what it means for us is that we all have to be constantly vigilant against our own cognitive errors and not rely on the luxury of explicit reasoning which might give us the impression that we are immune from the vagaries of our highly evolved brains, brains which are evolved primarily for survival and perhaps have philosophical musing as a latent function.