Is there only the one available (from The Black Gate) in the download?

Unfortunately, it seems so. Serpent Isle's Clue Book is called "Balancing the Scales" and features the familiar serpent picture on the cover.

If you're really interested, SI Clue Book isn't that expensive and is commonly seen on eBay. Prices range from 10 to 30 USD usually.

It seems that the missing cluebook and map may be added to the GOG package as soon as next week, if a comment over at Ultima Aiera can be believed.

Until then, the Aiera also has download links to the missing material: http://www.ultimaaiera.com/blog/so-because-gogs-ultima-7-complete-doesnt-include-the-map-and-cluebook-for-serpent-isle

The download is now called "cluebook" (used to be "cluebooks"), so I take it there's not going to be a Serpent Isle cluebook.

I really don't appreciate this. I bought the whole damn package because of the Serpent Isle cluebook (which I've never personally seen sold for 10 dollars on eBay) and now they have retroactively changed what's included in the package. I e-mailed them and asked to return my money if the cluebook is not included, and the answer was that it's going to be included next week. That was back when this game was released on GOG.

I agree that the GOG package should include all the clue books - after all, Serpent Isle's book is one of the easiest to find and they even got Ultima III clue book, which is quite rare and expensive.

At the moment there's at least one SI clue book on sale on eBay for $19,99 (about 15€) + postage. I don't think that's too expensive, but maybe that's just me.

However, if you're only interested in good quality scan (PDF) of the clue book you can download one from elsewhere, for example here: http://originadventures.wordpress.com/category/books/serpent-isle-cluebook/

All in all, it's still quite a bargain to get Ultima VII and Serpent Isle plus the add-ons for $5,99 even if they don't include the missing clue book later.

Paying $20 for a cluebook to a game that cost you $5.99 seems a bit much.

That's true, however I bought the set just for the cluebook (the Ultima cluebooks are kinda neat!). I don't really care about the rest because I already own the CD collection, and I prefer Exult over Dosbox anyway... Of course it's nice that I can get the SI book scan from somewhere else, it just bugs me that I paid GOG for something they were supposed to have, and didn't.