Heya there,
Ren'Py has a built in function that lets you encrypt/archive files into a single file, which I believe helps with beating the file limit!
I don't have Ren'Py directly at hand for reference, but I believe if you open up 'options.rpy' and look near the bottom, there should be a section where you can specify the file types you want to archive. Uncomment as needed and add all the file extensions you're using such as .png, .ogg and so on--and when you deploy the game, all the files should be packaged neatly!