You need to clean off the CPU and cooler and apply new thermal paste each time they are separated from one another. If you don't do this, the paste cannot do its job.
Can they degrade over time? Certainly. Pumps can wear down, causing fluid flow rates to drop. Fluid can break down and clog up pumps, radiators, waterblocks, etc...
Radiators get dusty and need to be blown out every six months. Remove the fan to blow out the radiator with a can of compressed air. Blow the air from the inside of the case to the outside.