HI mikazakov,
I'll jump in here and add what I know about this setting, and the Autodesk folks can correct me if I'm off base.
I typically recommend setting this to No even if you are using unique file names (which I also recommend). This setting doesn't really enforce unique file names, it merely searches for them. So I find it to cause more problems than it solves.
Where I find it to be particularly problematic is when I rename a file in order to purposely break a link so that I can resolve the link to a different file. For instance when working with derived parts and trying to point the part to a new revision of the derived part file. If Using Unique File Names option is set to Yes, Inventor searches every folder/file in the project and takes a long time to tell me what I already know: the file can't be found. However, if I set this option to No, Inventor immediately throws the resolve file dialog and allows me to redirect the link.
I've not noticed any problems with setting this option to No.
The Help files do not document this setting well at all.
I hope this helps.
Best of luck to you in all of your Inventor pursuits,
Curtis
http://inventortrenches.blogspot.com/