If you're looking to change the fonts on the stock Reader's menu you'd have to open up and muck with the Reader app (Reader.apk) itself. If you can modify the Reader.apk it's possible to install the modified version using SDcard-based ClockWorkMod recovery without rooting the Nook.
Alternatively, you can embed or link alternative fonts to the ebooks, see
https://www.mobileread.com/forums/sho...d.php?t=178623. I used to do this for awhile (to make use of fonts that can display my native language character set) using a Calibre plugin
http://phanquochuy.me/?p=114 (but it got old quite fast so I simply just switched from the stock Reader to Mantano Reader).
If you're looking to use a different font so as to display some international language character sets, see
http://forum.xda-developers.com/show....php?t=2092516 for some info/pointers. FWIW, the NST rooting tool Nook Manager (
https://www.mobileread.com/forums/sho...d.php?t=178623) replaces the DroidSansFallback font with the updated font from jellybean to add support for extended characters.