The weirdness of the scoring is definitely intentional; I wanted the numbers to really blow up when you got far into the game (though maybe I went a little bit overboard).
And yes, all of the music and sound effects except for the sound clip of Juniper at the very start are done entirely in code. The Game Boy has some specialized hardware for playing sounds, and the code interacts directly with that.. It takes a little getting used to when you first get started with it, having to do everything from scratch, and there's a very limited number of sounds you can actually play, but it's fun to see things come together.
Anyway, I really appreciated your comments. Thanks for spending time with my game, and for the kind words and detailed feedback! I'm so glad you enjoyed it!