Yes, the autosearch algorithm will skip sites that either
1.) have been searched to at least level 1 in the path in question, or
2.) have 2 or more sites there.
I really like searching with roving mages, especially early on when a +2 gem boost is really significant. It helps fund those expensive site-searching spells later on.
But of course it depends upon what mages you have access to (ideally multi-path), and on your playstyle.
-Max