Having got a Premium subscription again for a while, I notice the dictionary in the learning centre has audio files with some entries (by no means all but it's a huge task and I'm sure it's slowly expanding)
The books I mentioned earlier that attempt to mark pitch accent are
Colloquial Japanese, Clarke & Hamamura, Routledge 1987
The title is very misleading as its part of a series Colloquial French, Colloquial German etc. that actually teach standard language rather than what I'd think of as colloquial. The series is still in print but I don't know if the current edition tries to mark pitch accent. I'd hope they'd be using kana rather than romaji by now.
The romaji is typeset using acute accents to indicate rising pitch. and strikethroughs to show devoiced vowels.
Japanese Step by Step, Gene Nishi, Mc Graw Hill 2001
Also tries to mark pitch accent using Capitals and underlines. It is very distracting to read.
An older book I have
Japanese for Beginners, Yoshida et al, Gakken 1984
has a short section using musical notation.
Also of note are the graded readers
レベル別日本語多読ライブラリー にほんご よむよむ文庫
http://www.ask-digital.co.jp/tadoku/index.html
While obviously pitch accent isn't marked, they come with a CD of the stories being read aloud. So as well as reading practice you can improve your accent and listening skills.