Figuring out if an led strip/matrix has a short or not with a multimeter
I also have continuity from hot to ground.


This narrows it down.  Look at the solder joints (under magnification) where hot and ground are next to each other. Scrape away any solder splash. 

You would need a 4 lead ohm meter (milli-ohm) to find the short with an ohm meter. 

UPDATE


  When I have it set on 2000, hot and hot read 0, hot and data read 1,
  hot and ground read 1000.


The short is between hot and data, not hot and ground.