You will know a rotor is done when it causes shaking during braking. This is because they no longer have enough mass to keep heat under control. Therefore they overheat and either warp or get an uneven coat of pad material. In either case you will get noticeable vibration under braking. Cutting a rotor like this will only buy you a little time before it happens again. It's best to just replace the rotor.
If you don't have any shaking, then simply replace the pads and clean/lube the caliper slide pins. When reusing old rotors, simply perform a good bed-in procedure to reshape the pads to the rotors and you will be set. Personally I recommend OEM Honda/Nissin pads cause they've lasted me over 80k miles so far on our 03...
If and when the rotors do start to go bad (shaking), it's okay. Simply replace them with new ones, and retain your newer pads (provided the pads are still thick). Perform another proper bedding procedure, and your good to go.
BTW: Don't forget to replace your brake fluid every 3 years...
OEM pads can be purchased online for a discount at places like HondaPartsNow.com, HondaPartsDeals.com, HondaAutomotiveParts.com, and a few others for about $43. The kit (#9) should include pads, pad-springs, pad-shims and grease. Don't forget to replace the caliper hardware as well (#22 & 23):