For comparison, the `ls` in GNU coreutils is a single 5,310 line C file[0], so I think nnn's codebase pretty much par for the course (nnn has much more functionality than ls with 1K fewer lines of code). Splitting into different files makes more sense when you have a bunch of independent subsystems, but nnn is just a file manager. As someone who has dug through nnn's source code enough to track down a bug and propose a fix, I found it to be a pretty easy codebase to work with.
[0] https://github.com/coreutils/coreutils/blob/master/src/ls.c