1) "Everybody" who said clunking is "bad" would be quite wrong.
The clunking occurs during the gear change when the drive is not connected to the output sprocket, because the clutch is disengaged.
Motorcycle gearboxes are constant mesh and ratios are changed by sliding "dogs" (very coarse teeth on the side of gears) which engage with matching holes in the next, adjacent gear, or by engaging with splines on the shafts which hold the gears.
The only effect of the clunk is that a small amount of hardened gear material might be dislodged on occasions, but this is caught by the oil filter or by the magnetic drain plug. The clunking will not affect sprocket wear, or enable it, since it takes place while the drive is disconnected from the sprocket.
2) I'm sure there will potentially be more wear on the drive belt while towing a trailer, but it's not a big deal for the people who do it.
Have fun