Re the last of your post:
The bootloader isn’t overwritten during a user update process so bricking isn’t likely.
The FPGA hardware won’t boot without good CRCs. The DS (and DS Jr) will play sound indefinitely (almost) perfectly even if the control/display processor isn’t there or isn’t doing anything. The Jr also has the option of automatic input selection so the FPGA can be more independent there. The control processor is needed for the display and UI interactions. If the display is correct then the code is probably loaded correctly: any bad sound is probably caused by doing things too often or not often enough and generating noise. There’s also the possibility of it banging the crap out of the FPGA causing noise… But if we knew exactly what is going on it probably would be fixed…