Are locations unique? or can you have multiples of them. For example I have a few Wayne manors. Can I play 2 of them in my resource row and gain 2 endurance for exhausting a Gotham knights character?

Nope, Locations, like characters, are unique, unless a location says it's not, like Mountain Stronghold for example. If you had a Wayne Manor, and played another one, the old one would KO.

which would make you lose a resource.

You're also a bit askew on payment powers. For the sake of illustration, we'll say that you control Ra's al Ghul, The Demon's Head, whose continuous power makes locations non-unique; since you can now safely do so, you flip up two copies of Wayne Manor.

This doesn't let you gain 2 endurance for exhausting a Gotham Knights character; the exhaustion is a cost, and must be paid for each use of Wayne Manor's power. You would need a card like Spoiler, who has a triggered power, if you wanted to double up on that card and double up endurance gain.