to save some space, you can compress the code.bin or even create an ips patch. (for creating ips patch, after delete some strings in code.bin, you have to padding the those missing bytes with 00 and compress before creating an ips patch file.)
compress command:
Code:3dstool -zvf code.bin --compress-type blz --compress-out code.bin
I have tried an ips patch, but it didn't work. I made an issue on github. Hopefully they can help.