OK, a short history lesson
IE3 was capable of handling some javascript, but it was very very poor... Don't know about external .js files. It didn't support CSS as all. It didn't "understand" images[] array so image rollovers were impossible in it.
NN3 was a bit better - no surprise, they were the first to introduce javascript support. I don't know about support of external .js files. It didn't support CSS as well.
Starting from v.4 they both could handle scripts including external .js files using <script src=""></script>.
They both started supporing CSS1, but the level of this support and it's accuracy is very low. Both allow attaching external styles using <link rel=stylesheet href="">.
They both, if I'm not mistaken, didn't support @import CSS rule to attach external styles, and this technique is used to sepatate styles for newer and older browsers.
External script files is just another way to add JS to a webpage. And if some JS construction is supported, it doesn't matter how you use it. The same thing is for CSS.
Right now, the best CSS support is in Opera and Mozilla browsers.