Definitely let them know it's your honeymoon! We had it noted on our reservation at the Poly and when we arrived we promptly received a congratulations, the "just married buttons" and were upgraded from Garden View to Lagoon View! If a resort has upgrades to give, it seems that they often give them to honeymooners or anniversary celebrators first.
We did have it noted on our ADR's as well, but we didn't receive any pixie dust there. Lots of couples do though, and wind up getting free dessert and things like that. You never know!