After speaking to one of the team members, I'm opening this issue for a possibility for people to make items work as bait, such as maggots or worms from other mods through datapacks and CraftTweaker. One concern I have is that the new bait items would have durability now and may cause issues, I'm not sure about any of that though since I am inexperienced in coding and all this.

After looking further into this, there is no good way to implement this unfortunately.

The best way is to create an Aquaculture 2 addon, which adds its own bait. Only requires a few lines of codes - but would require one to be able to code of course.