Not 100 percent sure if this will happen but

I think the solution is simple: make nebulite crafting a mini-game.

A repeatable minigame that requires user input, and the more you do it, the more your crafting level increases. The higher your crafting level, the higher your chances of getting a higher rank nebulite.

That way botters are completely cockblocked, players have to work for the nebulites and it's a fun new thing to play with. Plus it's an easier way of getting nebulites than what we have now.

Except there are still programs that would allow hackers to go through several parts of a minigame automatically, which is likely one of the reasons why no minigames today reward any items. This would just cause them to move from botting to strictly hacking, making it impossible for GMs to ban them as there's nothing to catch.