Does Yogacara deny atoms exist or does it just say that atoms are just appearances? Vasubandhu seems to make arguments in this article against the concept of atoms to prove all is appearance in consciousness. But doesn't this go against modern science,even if his arguments are logical? I mean modern science says that atoms exist.
This idea is well known in Mahayana literature, one could say it's a standard idea. What the argument is about, though, is not whether atoms exist at all, but whether they exist as something substantial. Similarly, we are not questioning the existance of rainbows, rainbows do happen - they just don't exist as something solid one could touch.
You won't argue that atoms are not solid nor made from smaller pieces of matter. Even the planetary model is a vast simplification. And of course, the elementary particles that atoms are made from - are not substantial either.
The point of the argument presented by Vasubandhu and others is that as you go down to the microscopic level, you won't find any matter, nor anything substantial at all, nor will it be static and stable, as everything under closer examination is a dynamic system made up of something else, of some interactions.