They only appear where you can see, I do believe. I also believe this is so that you researching a new resource does not screw up cities elsewhere who cannot see the resource (but would not be able to build over a place that contained it)
There is actually a bug that causes resources you can't see to block resources.
I personally strongly suggest to stardock that they create a 'mysterious resource' tile that makes it evident that a resource is there rather than just being frustrated because one cannot build buildings on certain tiles. This is most commonly a problem when I build my city where an enemy city used to exist. I've had situation where I take over other cities and find myself unable to build more than like 8 buildings, or 2 big buildings, because they are surrounded by stuff my faction cannot use.
It could be like an event. "Sovereign XXX discovered a new resource. word of its presence has spread to your kingdom/empire. Perhaps we will find a way to utilize it in the future."