Atomic diagrams would be good for advanced societies, but societies in the bronze age or middle age advancment are the ones that we have to worry about. They won't understand atomic phyiscs but they are capable of excavation. Any fancy symbols might just intrigue them.
I think they underestimated the intelligence of possible future societies. Any society advanced enough to excavate this will be intelligent enough to ask "what does this symbol logically mean". They won't be limited to the 'bad-vibes' that the current ideas are heavy on (language aside).