They clearly and easily can. A speedster like the flash vibrates trough objects by abusing the idea of matter at atomic level being basically 99% empty space. So they vibrate the molecule of their body at the right frequency so to be able to move them into this empty space.
Flash can easily vibrate through a lot of high density things, like metals for example. And this makes a lot of sense anyway: the moment atoms are so packed together that the space between them become impossible for a speedster to vibrate through, then we have a black hole and Flash has way bigger issues to care about.
Now, let's come to our Kryptonians. Are they made of black holes? No, totally not, not even in the wildest canon ever written. The average Kryptonian is, according to official canon, simply a tiny bit denser than an average human being; something around 100 kg of weight by 190 cm of height. Is the average human being denser than metal? No way. Is an average human being denser than a wall? Nope. So, yes, a speedster can easily vibrate through a Kryptonian.
Not taking into account that currently 99.99% of Kryptonians are in the form of space dust, so their density is quite low anyway
The Flash, thank to his connection to the speed force, which is basically "the material speed is made of", is the fastest thing in all creation. If something can go extremely fast, the Flash can still go faster, 'cause he is speed itself. He is so fast that his punches can hit with infinite energy, he is so fast that he can see the flow of time, he can think so fast that he is practically the smartest guy in the universe. Thus he is often depicted as the stupidest guy in the Justice League, he get beaten regularly despite being impossible to hit, he slide on ice, has very high reflexes only when they are not needed, and so on.
Now enter the teacher's pet, Superman. Flash could annihilate Superman in a blink of an eye, according to the official, canon powers of Flash, if it wasn't for a simple power Flash has not: Superman is DC's darling. So no matter how counter-canon or ridiculous or plainly wrong the story turns out, Superman wins.
So, in conclusion:
- Can a speedster vibrate through a Kryptonian? Yes, easily.
- Can a speedster vibrate through a specific Kryptonian, Superman? Yes, but only if it's for comical relief.