As far as I know, no one makes aftermarket flares for 1st generation frontier. The fender flares from an 01-04 crew cab will be a direct replacement on your 2000 crew cab, so long as the rear flares from from a crew cab shortbed. I can guarantee you that all crew cab shortbed 1st gen frontiers use exactly the same bed and installation of the rear flares will be as simple as pulling the current ones off and popping the new ones in. On the front, I have seen someone put 2000 frontier flares on an 01 frontier and they just popped right in with the plastic rivets and the screws a long the bottom edge lined up. You should have no issue with installing the fender portion of the flare. For the smaller section of the fender flare that goes over the bumper valance you will need to do some trimming. The 01-04 flares are obviously "taller" and will interfere with the chrome bumper on your 00. You will likely need to trim a small amount of the plastic to allow it to sit over the chrome bumper better --->
Just some disclaimers for you, the bottom portion of the flare that sits over your bumper will not sit perfectly flush with the valance as on a 01-04 as the profile of the bumper is different. You may be able to fix this by just putting a couple extra screws on it. Number two, It will be quite difficult to find new OEM replacement flares and its possible the only you will be able to them at a junk yard.
And to try and give some validity to my comments, I have done two frontend conversions on frontiers. One on mine to an 02-04 Xterra and on another from a 2000 to a 2001-04 frontier frontend and I also swapped a 2000 frontier frontend onto an 01 xterra.
-Dan