While your console will continue to boot without boot9.bin on the SD card (because boot9strap is already installed in the CTRNAND), you will lose the ability to perform advanced recovery operations via GodMode9.
It contains the "keys" (cryptographic seeds) used to decrypt almost every piece of encrypted data on the system, including games, system software, and the bootloader. Why is it Important? Boot9.bin 3ds
If you have a hardmodded 3DS (soldered wires to the NAND chip), boot9.bin allows you to decrypt a NAND backup on your PC. If your 3DS is bricked, you can use boot9.bin with tools like 3ds_nand_fat16_imager to manually repair the system partition. While your console will continue to boot without boot9