Basically, PowerTools Lite doesn't delete anything. You do the final call what to delete. By default, PowerTools Lite lists all history and MRU data for deletion, this is clearly stated by the program. Log files of Yahoo Messenger are, by definition, history data.
You can, for example, use the Ignore Words feature to make the program not to list these items.
Also please see this: http://www.macecraft.com/phpBB3/viewtopic.php?f=23&t=3799&start=0
