I have two platforms to monitor. I want to create one application that I can apply to all hosts that come on board. I know that Spunk will not scream anymore with 6.2.x, but are there adverse affects? Will it create errors in the Spunk log files?
You won't see any errors, not finding a file is expected behaviour. You also won't see any performance issues if you keep the number of monitors reasonable. You might see unexpected indexing if one platform one day happens to create a file in a path that exists in the other platform.
For clarity, maintenance, extendability, fewer cross-platform dependencies, etc. I'd advise to create two tailored apps nonetheless.