In automatic firearms, the magazine is the weak link.
When the gun gets cleaned, the magazine gets cleaned.
My guns get cleaned every time they get fired, whether one round or 100, so the mags get cleaned too.
If the magazine has picked up lint, dust, carbon from firing, lead bullet lube fouling, or gets dropped, it gets cleaned whether the gun is cleaned or not.
Cleaning magazines is non-harmful. There's no reason at all not to clean them.