The amount of kilometers (miles) on the engine should be one factor. If you have an engine with high mileage then it might be wise to have a machine shop do the work. However, if the mileage is low then just lap them yourself.
When I re-built the top end a few years back, I lapped the valves myself. My bike only had 18000 kms (11000 miles) so, in my view, my engine was not excessively worn. I now have over 28000 kms and my engine still runs like new.
Have you checked the side play for the valves? You measure that with a dial indicator, and if its out of spec then you need to replace the valve guides.