Recommended? Yes. The '03 forks are 48mm and seem to enhance steering precision. It's not a night-and-day difference, though. I plan to get both ends of the suspension re-valved and it didn't make sense to put time and effort into the stock '00 fork when it wasn't all that expensive to swap in an '03 fork and go from there.
Some side notes on the '00 KX125:
--The stock rear spring is progressively wound, which has the effect of raising the spring rate as the shock gets deeper into its travel. That's fine, but when a progressively wound spring is coupled with a rising rate shock linkage, it results in a rear suspension that kicks instead of absorbs. I have gone to a straight-rate spring and have realized an immediate improvement.
--The stock front brake is mushy and weak. Pitifully weak! I swapped an '03 master cylinder onto my handlebar with good results. Braking power is much better, and the feel at the lever is firm and predictable. I'm still using the '00 caliper and rotor.
--From what I've read, the '00 model had the best stock cylinder porting of the '99-'02 L-series KX125's. I can't comment on the other model years, but I can tell you I like the power delivery. I have a Pro Circuit pipe and an FMF TurbineCore 2 silencer/spark arrestor. Overall, it's a very linear power delivery with a bit of a hit in the upper midrange. Easy to ride.