Should you place accents on letters in academic writing in English? Is there a standard practice in academic writing regarding the use of accented letters when the underlying language is English? I'm specifically thinking of the word naive, which often has a dieresis above the i, but I suppose this is applicable to other words.

I would prefer to not use them since it's simpler and seems somehow less pretentious to me.

Also, is there is a difference between dissertations and journal articles?
Do you like reading papers with misspelled words, grammar errors, uncertain syntax, badly formatted equations, unreadable graphs and unclear pictures? Probably not. 

Modern typesetting systems and careful proofreading allow writers to avoid, as much as possible, the above unpleasantnesses and, moreover, allow them to typeset all sort of characters. Furthermore, macros and shortcuts can be defined for quickly repeating difficult words. Thus, with modern typesetting systems there's really no excuse for not using diacritical marks, regardless of practices which date back to an epoch when typesetting systems were not as flexible as modern ones. 

Academic papers and books are not only read by native English speakers, but by people from all over the world, where a missing accent can be cause of confusion or, in case of many missing accents, considered a sign of sloppiness (which typically does not put the reader in a favourable mood), especially if the accent is missing from a proper name.