Is it just me or are the published articles a strain on the eyes in general? Has there been(/shouldn't there be) a study on optimal font sizes for reading?
This is a historical anachronism. The fonts are chosen for the print version of the journal. For a print version, if you use a smaller font, you can squeeze more text onto the same page and print the same paper on fewer pages -- which saves money. So, for print publications, the small font size arguably makes sense. However, today print is less important and the digital format is more important, but journal requirements haven't caught up to this fact.
For instance, in computer science, the ACM is a notorious offender: they require papers to use 9pt fonts, which are very small.
Journal prescribed fonts haven't really caught up with the digital era. They were optimized for a time of print, where each page had a price. Unfortunately, researchers are required to use fonts specified by the publisher at a conference. But many people usually upload a more readable version on a web page or the arxiv - 11pt tends to be reasonable.
I prefer the old-fashioned way of reading papers: print it and read with text-marker, and I find the usual font sizes OK (sometimes too large when printing on A4 paper). Margins of ca. 4 cm per column are (would be) nice, though.
Monitor space is much too valuable for more than taking a glance which paper exactly I want to get from my collection. Where should I edit notes, do calculations and see graphs/images/man pages if most of the monitor is taken up by the paper?
I did print much less when I had 2 monitors, but at my new place I have only one. And anyways, no monitors can hold as much easily accessible information as a bunch of papers laid out on a large table.
(But I LaTeX my papers, so whoever wants larger fonts is welcome to rerun them with other settings).