I suggest archiving the files so they're not too many.
I use Ren'Py for my vis novels too so I know.
Here is some code you can use:
init python:
# Declare archive files
build.archive("scripts", "all")
build.archive("images", "all")
build.archive("audio", "all")
build.archive("others", "all")
# Put script files into the scripts archive.
build.classify("game/**.rpy", "scripts")
build.classify("game/**.rpyc", "scripts")
# Put images into the images archive.
build.classify("game/**.jpg", "images")
build.classify("game/**.png", "images")
build.classify("game/**.webp", "images")
# Put audio into the audio archive
build.classify("game/**.mp3", "audio")
build.classify("game/**.ogg", "audio")
# Put other files into the others archive
build.classify("game/**.ttf", "others")
build.classify("game/**.txt", "others")
