I noticed that later resources like Niter, Coal, Alumunium, etc. were already able to be harvested, even if the resource icon was not even visible on the map yet. I've now changed the required tech to harvest a resource to the same one which triggers the visibility of the icon.
However the harvest action icon is still visible if there's a resource underneath your builder, even if it's not discovered and harvestable yet. So theoretically you could scan your whole territory for any yet undiscovered resources if you really wanted to. I don't think this is a major problem though. And it also works only in your own territory, and not on neutral ground.