What you are hearing is transmission gear clack. You will likely notice a change in timbre or intensity when the clutch is actuated.
The power transmission gears are always meshing, even though they are spinning on a shaft when not engaged and passing power. They still have mass and inertia, so they change tooth contact sides fore and aft when there are any speed changes of the crankshaft.
If each cylinder's power pulses aren't exactly the same, the crankshaft changes rotation speed between cylinder firings, causing the gears to clack as they change tooth face contact. Higher RPMS smooth the inertial pulses/frequency. And adding or removing clutch mass with engagement/disengagement changes the pitch or harmonic frequency.
The answer is to make all the cylinders fire with the same intensity. A thorough and precise tune up, as well as a vacuum sync will usually clear up most of the clack at idle. You can also fine tune the pilot screws to minimize. But, that is a pretty fiddly opperaion.
The clack itself does not indicate any impending mechanical failure. But, it really should be avoided as it does increase wear what with all the parts bashing each other instead of sliding gently.
My 77Cb550 F will make that same noise when it is tune up time (In fact, all the Cb550s will). Precise ignition timing and a good tune-up per the 3K schedule quiets it down spectacularly.