cephalo
Deity
well then something in the script changed that.
Every map I have played on, copper, iron, horses (and some food related bonuses that are always revealed such as sheep, corn, etc) are never on a tile with forest or jungle.
I don't know if forest and jungle spread to those tiles during the game (TBH I've never payed attention) but when the game starts it looks like this:
before
after
before
after
Well according to these screenshots, there are some clearings that are just empty. You still might guess wrong if you plunk down a city.

The reason for the clearing is that the XML rules don't explicitly allow trees/jungle for that resource. If a resource does allow them, they should be replaced if they were removed to put a resource there. I like the massive forests because the climate conditions in those places warrant them, but I don't want it to prevent resources from going there, as that used to be a big problem.
I know this is something that always bugged you. You might try changing the XML so that the hidden resources allow forest/jungle. That way these holes should be covered up.
Edit: However, since I'm already cheating by putting them there in the first place, maybe covering them up again will not have any negative consequences. I should try this in a future version.