I think the sort of people who are looking up scientific articles would almost entirely be the same sort of people who appreciate information density and hate useless whitespace.

Your first and second points could be satisfied by showing a small PDF icon where the thumbnails currently are. Whatever size that allows the listings themselves to be as close together as possible. The PDF icon could also be different colours depending if it has a paywall, or an money symbol over it.

The really big thumbnails that mostly all look the same make the site look very amateurish on first sight.