I heard a story from the days of the Game Boy Advance, which supposedly had a similar feature.
Physically, custom carts could easily be made. To prevent this (from a purely legal standpoint) Nintendo made it so the GBA internal ROM was looking for specific data (validated by hash of sorts) on the cart, or it would reject it and refuse to boot. This data happened to be the (copyrighted) logo displayed on boot, hence it made unapproved carts either unbootable or illegal.
Reminds me of how, back in the day, software would look for the letters "IBM" at a specific ROM address (it was in their copyright message) in order to identify the video card as a VGA card (or maybe it was back in the EGA days, can't remember). One of the clever clone card manufactures put in the ROM "There are various pieces of software that expect the letters IBM to appear here".
There were still boatloads of counterfeit GBA games, particularly Pokemon. If you bought any used Pokemon games, odds are very good they were counterfeit.
That's an open-and-shut case (provided they catch the bootleggers). This was meant more to (theoretically) stymie something like Tengen's 3rd party NES carts. Nintendo wants a cut on all the games that play on its consoles.
Physically, custom carts could easily be made. To prevent this (from a purely legal standpoint) Nintendo made it so the GBA internal ROM was looking for specific data (validated by hash of sorts) on the cart, or it would reject it and refuse to boot. This data happened to be the (copyrighted) logo displayed on boot, hence it made unapproved carts either unbootable or illegal.