It is more likely "on" a shelf or "in" a drawer.
If you do hear "in" a shelf, then I would visualize a rather short shelf, almost tightly confined, open only in the front. We might call it a "nook" or "cubby." Think, perhaps, of shelves in school hallways designed only for kids' shoes; one shelf per pair of shoes, very small area. That's because the "in" suggests a tighter confinement than is suggested by "on."
Student or Learner