With no disrespect to lilypond-book, use LP to create unadorned PDFs,
pdfcrop to crop them, and then put it all together in a modern LaTeX
like pdflatex or lualatex.
In the -user archives I've read that some include the PDF generated
by LilyPond. And then, I guess, they still use LaTeX to add images,
text and page numbering.
Exactly. Another good reason is the reduction in complexity. You can
concentrate separately on getting each cropped PDF just as you want it
before worrying about its placement in the final document.