Eliminating the duplicates makes it much easier to search the history for a command that was used long ago instead of having to skip over hundreds of duplicates of some non-interesting command, such as "ls".
It also makes it much more likely that complex commands used a long time are still preserved. No matter how large you make your history file, it is much more likely that it will become filled with simple commands that you do not need to recall from history, instead of keeping the complex commands that you hate to retype.
Moreover, while having a command history is useful to avoid retyping some commands, some may be less willing to preserve a history from which it is easy to discover which have been their exact actions while using the computer, though for this it is preferable to also disable the saving of the history file.