Flagstone was included in the game to make the roads, so that people wouldnt deconstruct them and get tons resources at the very start. At some point Tynan made other types of roads that werent from flagstone so it doesnt make sense that they no longer return resources.
To add to this, I think they look pretty neat, even more than normal stone, so they could receive at least +1 beauty.
Edit: wrong section, sorry.
If you would give flagstone +1 beauty like the stone tile, the stone tile wouldn't made any sense anymore.
But to reflect that they don't give resource back but use the same amount like stone tile, they should cost less resources.
And for this issue allready exist some mods.