Having multiple HTML files inside an Epub file isn't a problem. You just treat the Epub as a directory tree of files -- HTML, CSS, images, whatever. It doesn't make the problem any more difficult.

As for memory usage... Yeah, that's a little trickier. Having "War and Peace" as a single HTML file might be kind of taxing. I admit that I haven't looked into WebKit to see how it handles large files. At worst, though, you could break the HTML into smaller temp files and render them independently.

I'll have to see just how much of CSS is supported by FBreader these days. It's been a few versions since I've tried to do anything with it. I have been using FBreader for Epubs and agree that it's usable in its current state. CSS support would make creating my own books from scratch much, MUCH easier!