Are diamond treatments like laser drilling and filling permanent?
It depends on the treatment. Laser drills are very difficult to see with the naked eye, but fracture filling is pretty obvious (to me, at least).
Some treatments (like drill holes) are permanent, whereas others (silicone fillings) are reversible - they can be melted out.
I'd avoid clarity enhanced diamonds. The secondary market (should you ever decide to sell it or trade it in) is a tiny fraction of the natural diamond market. They just don't hold value as well.