Well, not even to stop them claiming them as their own (I doubt most GBA pirate cart manufacturers at the time were putting their name on anything) - just to stop them selling copies without any money going to Sintax.
Every licensed GBA game got pirated instantly, Nintendo just didn't care so much (their focus was mostly on Japan, North America, Western Europe etc - places where pirate carts rarely surfaced and Nintendo could easily sue if they did) - but Sintax were competing with the pirates in the same markets, so if the same thing happened to them they'd be kinda screwed. and Sintax couldn't exactly take other companies to court over games that infringed a ton of copyrights already, so they had to protect their stuff through technical means.