Bought this car used, 2004 Mini S. Rear hatch seems to collect water in it when it rains, as in inside the hatch body itself, not inside the car.
when I open the hatch, water that is sitting in side of it drains out when inverted.

I am guessing it's likely entering via a bad seal for the spoiler, the 3rd brake light or both. Do these have seals/gaskets? or should I just be removing and doing a good caulking job?

 

Mine started leaking through the exterior grab handle. The gasket went bad and the collateral damage was the contacts for the license plate bulbs.
It can also make its way through the 3rd brake light but you'll see a cracked lens if that's the culprit.
The seal around the wiper arm is also prone to leaks.

It should be easy to find - remove the interior panel, close the hatch and have a helper soak the outside with a hose while you're inside the car.

 

Leaks in the boot are too common.

My third brake light leaks a little--have watched several drops of water coming down the inside of the glass below it, but it never appears to be much. I removed the third brake light to inspect. I did not find a cracked lens. I did find that the gasket was irregularly compressed. With only three screws holding the thing in, it's no surprise.

I have heard the theory about the handle gasket. I have one on order to replace it.

 

I used silicone sealant along the 3rd brake light after replacing it with a new unit.