I wanted to make custom sound effects for my Bomberman 3DS Revival Project. Is there any way to make custom sounds? If so, is there also a way to use them for the game?
Not really.
You can kinda make a sound effect using MML if you're fine with using one of your custom BGM slots for your sound effect though
You can use WAVSETA. There is a WAV to SB WAV converter here that you can use to bring audio files to SB, then you register it with WAVSETA and use a BGM slot to play it.