The questions currently being asked at HighRanking Forums are:
(1) Does a search engine index a password protected (on open document) PDF document? (2) Does a search engine index a print & edit protected PDF document?
One would assume that in the first case, of a view password protected PDF document, the search engine would not index the document. In the second case, one would thing the search engine does index it, but does not provide a cache of the page for HTML view.
The tests are currently being done and the results will be posted at the thread.