Syag is absolutely correct that if an expectation or social norm exists, no punishment would be necessary to induce students to clean up after themselves. It is also true that if one does not exist, a punishment would not be especially effective.
I cannot explain how it happened that in many Shuls and Batei Medrash it is socially acceptable to leave seforim out. It is, however, self perpetuating. People do it because people do it. In this way, it is similar to talking during Davening, speaking Lashon Hora and so many other issues.
When I was in high school, the Rosh Yeshiva (who was recognised as one of the Gedolei Hador) would stand at the door of the dining room at the end of meals. If he saw a boy walking away from the table without his plate, he would fix the problem.
My own (elementary age) students know that in my classroom, making or leaving a mess is simply not done.
With all this said, and at the risk of sounding somewhat repetitive, I feel the need to point out that it is far worse to denigrate an entire class of people, be it those who use the seforim or their Rebbeim, than it is to leave the seforim out.
To be sure, it is perfectly fine to raise awareness on this issue, but let’s please exercise caution as the conversation continues, not to descend into the wholesale character assassination of Lomdei Torah.