How should I refer to non-permanent Web Pages, via Web Pages saved in PDF format?
I think that there are three main cases to consider here:


The web pages are aggregated data, e.g., in your example of a study that quantifies change over time.  Collecting web pages as data is routinely done in scientific studies, such as complexity studies that track a lot of pages.  In this case, the pages are not generally cited (and any data from them is likely to be at least partially abstracted and de-identified, to deal with a variety of legal issues).
An individual web page is a subject of study, e.g., for literary or intellectual criticism.  In this case, the standard references to the URL with time accessed is appropriate, along with block quoting of critical passages as part of your analysis.  You should save full copies yourself, and share them upon request, but likely cannot publish them unless you obtain permission or unless the source has explicitly adopted a copyright that allows republication (e.g., Wikipedia).
The web page is being cited as a scientific work (some overlap with the last case).  In this case also, the standard reference of URL with time accessed is appropriate.  This is unusual, since most scientific works go into archival papers of some form, but does happen---I've certainly done so, when that is actually the right document to cite.  This should still be a document with some expectation of longevity, e.g., a blog post on a scientist's established site, the archives of a mailing list or discussion group, a manual from a piece of software's distribution site.