The issues element is an entirely separate part and need not be/doesn't run when you run the temp cleaning (main) part of ccleaner.
I use a diferent program for playing/cleaning with the registry (a specialist registry cleaner), 'Government Health Warning editing the registry can seriously damage your health (system's)'
So you are wise in leaving what you don't know alone, redundant/empty registry keys may increase the size of the registry files and may contribute to registry file fragmentation which may have a slight performance hit, but they rarely do any harm.