The thing is, you read a novel in a linear mode, and need to skip back and forth in a reference book. That makes it more practical to keep reference materials (including game manuals, for instance) in a random-access format like a book, while you can curl up comfortably with a Kindle or a Nook and read a novel without much change in your reading habits.
Half of the reason that digital reference books aren't quite ready for prime time is that nobody's properly formatting them with e-reading in mind. They need copious hyperlinks, at minimum. Better chapter division -- the things should have tabs down the right side, like a big dictionary does. Bookmarks need to be enhanced.
On the flip side, e-readers need a redesign to be MORE reference-friendly. Multiple windowing capability would really cut down on the flipping-back-and-forth issue.
There have been a couple of designs with two tablet-like screens that clamshell together like an actual BOOK, and they were specifically intended for textbooks and the like. Alas, the KNO never went into production, and the eDGe (tablet on one side, e-Ink book reader on the other) just tanked.
There's no real point or conclusion here; I'm just pondering.
Addendum, 06 MAR 2014:
the_gneech asked a great question:
"What is Wikipedia if not an electronic reference book?"
And that got me started toward the beginnings of a thesis. I put enough thought into this that I figured it belonged in the main body of the post:
[Wikipedia is] the exception that proves the rule! It's extensively (exhaustively) hyperlinked; it operates in a browser, allowing for multiple tabs and windows (at least on a proper computer; not so much on tablets/phones); incorporates media and graphics smoothly and dynamically ... in short, it's what a digital reference book SHOULD be.
(Unfortunately, it requires a continuous internet connection, and if you've got an e-paper style ebook reader, you're SOL.)
I will note that I never bothered to pick up the 3.5 edition of D&D. I found The Hypertext d20 SRD to be far MORE usable than physical books. It's also available for full download, so you don't need a continuous internet connection to use it -- I think you're still out of luck with e-paper readers, but it's a situation where laptops are really more convenient than a tablet-shaped device.
Again, though, it's an exception that proves the rule. It's a fan-created work taking advantage of the Open Game License. When RPG companies release "digital editions", they're invariably PDFs, formatted for printing: entirely static, rarely taking advantage of the PDF format's ability to create sections and bookmarks, and, worst of all: they're laid out in portrait mode, often in two or even three columns, making it difficult to see an entire page on-screen, and requiring constant scrolling back and forth to read through a section.
I realized at some point that my vague desires for a tablet are largely because I want to be able to read portrait-formatted PDFs comfortably -- but the font sizes used for most game books make them difficult to read at full-page size even on large tablet screens.
I think the take-home message is that if you're really looking to REPLACE reference books, you have to do something more than just dump the print version into a file.
I should note that the online hypertext versions of the Pathfinder SRD and the Mutants & Masterminds SRD don't have quite so nice a layout or the clean, simple code of the The Hypertext d20 SRD. They're useful SUPPLEMENTS to the physical books, but they're just enough ... off ... that I can't quite see using them as my main resource like I did with the last.