I've got a 97 125 with the conventional forks and like them alot. They are beefier than inverted forks (current inverted are 48mm (I think) and the conventional showas on the 97-98 RM are 49mm). When the seals go, the fluid doesn't just drip out the tube due to gravity and get all over your brakes. Keep in mind that RM model bikes are built for competition, so the forks are much better than those on a regular trail bike.
I've read this tuning guide for the 97 RM (and other bikes of that year) from Eric Gorr's web site that seems to indicate the forks were well liked and needed only a change in oil level for improved competition performance...
link here
Of course, newer bikes are going to be better due to technology advancements, but if you're just out to have a good time / learn to ride, that will make a fine bike.
FYI, I got my 125 for $1500 just over 1 year ago in California ... which was a really good deal at the time -- had Pro Circuit pipe & silencer, re-sleeved / newly serviced top end, excel wheels, tag bars and I got the stand. I've seen some 97-98 250s with asking prices of 1800-2100 recently, so 1500 is a good deal, especially with all the goodies for that price.