It’s really just semantics. Technically, you can’t say that the 97SE had prequel references because the prequels hadn’t come out yet.
But if you modify your wording a little, you could simply say that the 97SE contained elements that were intended to tie in with the upcoming prequels. So maybe instead of calling them “prequel references”, we can call them “prequel tie-ins”. The inclusion of Coruscant in the 97SE of ROTJ is a prequel tie-in.