Every mod I have done on this forum has been dyno proven with before & after runs no placebo guessing here, one can gain up to 8 extra HP from air box mods proven fact. Modifying is a personal thing so I am not going to try & convince you to do anything, all I have done on the forum & many others is provide the facts.
Your bike will run fine with the K&N filter with the extra holes drilled, if you want the full effects of the extra air intake you need to fit a fueling mod, more air more fuel more HP & Torque, we have had thousands of XT660 forum members running the same setup as your bike with no problem over the past 5 years. We have guys running stage 2 filters with no fuel mods & have never seen any engine damage in the long term. But I do recommend fitting a fuel mod when opening up the air box.
If you want a completely standard bike buy some rubber grommets from your local hardware & plug the holes up, remove the K&N filter & buy a paper Yamaha standard filter, it is a major job to swap over a air box about 2.5 hours worth of work.
Have a read here to see proven Dyno HP gains.
http://www.youtube.com/embed/Te0V71sGoxA