I didn't say it was a special "security chip", just a chip that handles the security. It could just be the CPU for all we know, but it has a region-lock clause in its use.
I'm not saying that Nintendo shouldn't remove legion-locking (they shouldn't have included it in the first place.), but it's more akin to this...
Lets say you setup a special password system that incorporated numbers, symbols, capitals and letters requiring one of each and tell all your clients that this is what is going to happen. You sign very good contracts in your favour for the usage. You use it for 2 years.
After a while, you realize you don't need one of each. However, you're no longer as profitable as you once were.
Do you dare change it, even though you signed contracts with said companies already that this is what you were going to do? What happens if only a couple of them agree to it, and others demand other changes as well before signing? It would be pretty worthless to only have a couple of them to agree to the changes.
Maybe keeping status-quo would be the best solution? That's what Nintendo needs to analyze in these situations, and why lawyers are so hated (on both sides).