Here;s some pics of the frame rail of a 99-04. This is the middle hole between the two K-member bolt holes. As you can see from the pic, it's wide open into the box frame of the rail. Hard to photograph, but i can definitely tell you any moisture that gets in here has a easy path to drain or dry out.
Go look on a fox body. There's a center sleeve in this spot, and if you were to cut it open, various metal supports holding it and the two side parts up.
As to when this change happened? No idea. Those of you with SN95's might want to go stick a finger in your rail and see if this center hole has a support. I bet the change was around 1996 as i can remember seeing quite a few rusted 94/95's.