Extruder Clicking without Extrusion Problems
Even though you may have acceptable extrusion, any clicking from that area of your printer is likely to be a missed step on the extruder motor. This may be insignificant with respect to print quality, but as you suggest, it is an irritation.

If you are confident that your nozzle is clean of debris (which is likely), you could consider to raise the nozzle temperature a few degrees. If the nozzle is not applying enough heat to the filament, it may resist being forced through and a click representing a delay, allows that much more heat to be applied.

You should not have to increase by much, certainly no more than five degrees.  It's also possible that you can slow the feed rate a bit to accomplish a similar result.