Instead they come with something called a digital watermark. These watermarks effectively are little bits of data buried inside the ebook. It's a benign form of DRM that doesn't bother the average user. Unlike other forms of DRM, a unique digital watermark is created when each copy of an ebook is generated. This lets the ebookstore add something to the ebook which can still be to track down who originally bought (and then pirated) a particular copy of an ebook.
Similar tech has been used for some time now in music, documents, and other content, but Pottermore is the first high profile ebookstore to use it (that we know of).
In the case of Pottermore, the digital watermarks are almost certainly provided by Booxtream. eReaaders.nl has taken apart an Epub and identified the particular details as being the work of that Dutch firm. I also looked into this, and my findings match theirs.
In case you're interested, the digital watermarks use by Pottermore are serial numbers added to various files. There's a warning statement on the copyright page, but the true watermarks are slightly better hidden. You can find them as strings of text in the title element of some of the images. Also, eReaders.nl identified an element in the CSS file as being from Booxtream. I believe they're referring to "boekstaaf". That's the only element that is clearly not based in English. I believe it's a Dutch name, which for obvious reasons would likely have come from a Dutch company.
Update: I'm pretty sure the file names are also used as a digital watermark. I just got my hands on a second copy of HP1 and the internal files have different names.
Booxtream has been supporting a Dutch ebookstore for the past 18 months or so, and so far as we know Pottermore is the first major use of their technology. Let's hope it's not the last. Let's also hope they also added a more subtle digital watermark; the one I found is far too easy to remove.