Short Answer is Yes, as this scientific paper describes. I suspect however your real question is why, and the answer for that is that right now, we don't have a complete enough picture of materials science to know with any certainty.
That said (and I make these statements with the caveat that I'm not a materials scientist), on many different scales, we see this all the time. On the planetary scale, we see IO being stretched and its shape deformed by the gravitational forces around Jupiter, and the volcanic activity formed by that movement. Bending a small length of metal back and forth quickly often makes it warm in the middle and more subject to failure, so we know that kinetic energy does have an impact on metals and many other materials in the manner you describe.
As for the specific vibration frequency that would cause the most impactful damage to your spaceship, you need to look at resonant frequencies. There are a few interesting mythbuster episodes where they try to collapse a bridge or explore earthquake machines by exploiting this concept. Certainly from a physics perspective, these terms, if used correctly, would at the very least add plausibility to your scenario.