Bought a set of black clip-ons from a guy on the forum here and he failed to mention that they are scratched up  (the clip-ons not the bars). Now I'm thinking maybe if I powdercoat them the scratches wont be visible. Not happy about the fact that I gotta drop some extra cash to powder coat them but I dont want to put scratched up clip ons on my bike.

Powder coat is quite thick and can make them hard/tight to get back on.

More critical, the powder coat will be compressed and can gradually wear off - resulting in loose bolts/parts.
You could have all contact surfaces masked off during coating, but that might be expensive.

Maybe cover the scratches with a Sharpie pen....

Get them re anodized

After I posted this I thought Andoizing would probably be the way to go but the Sharpie is definitely an inexpensive fix and worth a try. 

Any powdercoater worth his salt will sit down and talk with you about what you want masked off before he even touches the parts anyways.

I reanodised mine recently - was relatively straightforward.

See http://www.ducatimonsterforum.org/index.php?topic=55387.0 - the test piece is my clipon bracket.

most of the scratches are probably covered by the grips and the electrical parts so unless tis extremely visable... it might be cheaper to just buy new clip on bars.

tape off the interior of the fork mount and the space your throttle tube will take up. write "no" on the tape and verbally tell them none in the threaded holes.

wash with soapy water when its done and you will be good to go.