Just changed the back wheel on my '99 GLX, confirms that i have drum brakes, which is what i thought. But, they are very rusty, bits flaking off etc. Is this normal?

Sounds normal to me, my Fabia's were like that wire brush and some hammerite sorted it.

drums are nice and thick, surface rust is nothing to worry about.

I imagine you're writing about the outside surface of the drum covers right? If it is, the easiest way to get them looking brand new is to scrape off the rust (a dremel works wonders with a sanding attachment), and refinish them first with a rust inhibitor and later some paint (preferably black so they don't pop out lookswise).