If being able to add aftermarket parts is your main concern, then hold off for a 1995 - 2006 model.
On the 1989 - 1994 E series, currently FMF and Pro Circuit offer one pipe, one silencer and one spark arrestor.
For fork springs, Race Tech 3647 springs will work, as well as their 3750 springs or spring kit (two versions).
The KDX200 RAD Valve is for 1989 - 2006 model KDX200's. A few other parts are 1989 - 2006, as well.
Some aftermarket bearing kits are available from PivotWorks.
Wiseco pistons are 1986 - 2006 for KDX200 models.
Cometic, Athena and other companies make gasket kits.
Aftermarket clutch plates are available.
Chains and sprockets are commonly available and the same as 1995 - 2006 models.
Aftermarket air filters are available.
There are other parts as well. You have made me reailze that there are not a ton of aftermarket parts that are available for the 1995 - 2006 models that are not available for the 1989 - 1994 models. Thanks for making me think.
For anyone who fails to think twice and type once, on 1995+ model aftermarket availability, I did mention "a ton" of parts for the newer models. :-)