Out of curiosity, do I need to clean the Update, Dawnguard, Hearthfire and Dragonborn .esm files? LOOT lists the number of ITM records, deleted references and deleted navmeshes for each of these files, advising to clean with TES5Edit. Should I do it to these particular .esm files, or is it only advisable for mod files? I do have the most recent of each of unofficial patches installed.

Yes, Bethesda's files are so dirty they require manual cleaning in addition to automated cleaning. Here is a link to instructions. http://afkmods.iguanadons.net/index.php?/topic/4110-manual-cleaning-skyrim-master-files/