Can scientists name themselves in the scientific name when they discover a new taxon?
The answer is that in general, self-naming is severely frowned upon in the scientific community, but the act itself is not disallowed. 

There have been at least two instances of self-naming recorded in literature, as stated in John Wright's book The Naming of the Shrew, page 34, where Jules Bourguignat named a species of snail after himself as Ferussacia bourguignatiana. The naming was apparently very poorly received (being referred to as taxonomic onanism), although I was unable to confirm this by locating the original citation. 

Another example was given in the book on Sigismund Hochenwarth who named a species of moth (now Syngrapha hochenwarthi) after himself (original citation here).