A reference card is the design amd or nvidia sends out. It's their original design before companies like sapphire Asus, MSI, etc design their own coolers for the product.
Yes, you can remove the cooler if you want and replace it with a better cooler.
You can lower the speed of the card so it's quieter, there are a number of things you could do.
Edit: in general I would never mess with reference designs. Usually the aib model is far superior.