I own a DIY Hypercube Evolution equipped with Tevo Titan extruder, Clone Chimera hotend and Capricorn's High-temp PTFE tube. I use RAMPS with Mega and A4988's.
During prints, my extruder motor randomly clicks. I touched the filament and during the clicks I'ven't felt any problems with extrusion. I looked at the motor shaft to control if it clicks at special angles or randomly, but it clicks randomly. My prints do look very good: clear and shiny.
Do you have any suggestions? (the sound really gives me headache)
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.