Of course, there was the infamous `document.write()`, when the document was loading and the document stream was still open, but this was more of a hack than an interaction model.
I'm also not too sure, if LiveConnect (the connection between JS and Java applets and vice versa) was already a thing, when JavaScript was announced. (I think, this came a little later.)
Edit: I've a Netscape JavaScript book from when this was still in beta. (My first reading on the subject.) It does mention applets on a single page and that you may address them per ID via LiveConnect in a single sentence. So this was already implemented, but it wasn't advertised prominently. The book is all about form based examples.
(The applications in this book were the same that were demoed as showcase applications by Netscape on their website – and probably represent a significant part of what these voices reacted to.)
I remember using Netscape Enterprise Server suite, but didn't realize it had a JS engine in it. I do remember Rhino from a little later (though the wikipedia says it emerged in the late 90s.) And I have relatively horrible memories of the Netscape guys integrating the Visigenic ORB in both the enterprise server and Navigator. I wonder if Rhino was what they stuffed into NES/iPlanet/Sun ONE.