1) Virtually all Gameboy Flashcarts will function in the Gameboy Pocket, and Gameboy Color.
2) Yes, you could. You'd need a Microcontroller, with on-board USB capability, OR a Microcontroller + FT232 Chip. The Microcontroller would have to have a program running that receives data over USB and flashes it to the FRAM/Flash Chip/EEPROM.