Having a ROM is only legal, if you dump it yourself, and never share it with anybody.
When you start sharing it, then it automatically turns illegal.
According to the DMCA you may own ANY backup of any media you own legally even if you download a copy. It is not illegal to circumvent the copyright protection, it is illegal to OWN any software that circumvents copyright protection. As long as you own a cart for an older game, I doubt that it matters whether or not that it works becasue the point is you have the physical cart. Law enforcement really isn't going to take the time to test whether or not it works to determine if you have an illegal copy. Mostly they would ask to see the physical cart, once shown would drop the issue. Source: I'm a criminal justice major and My wife is a business law major.
Frankly it would be as bad a move as Sony or MIcrosoft locking out used games on the next gen consoles, I can understand keeping piracy to a minimum, but bricking a console or handheld will make people more apt to jailbreak them and circumvent any methods that the company tries. The stupid thing with these situations is that Microsoft has been locking out xboxes for having a second FAN to keep the system cooler and not RROD. This is the same thing Nintendo has been warning against, I knew Miyomoto was a loon but he is too smart when it comes to business, and intentionally bricking console or handheld for people modding or even using a flashcart is a bad business move. The only reason I want flashcart myself is because I want to play my old Zelda games on the go, I have so many doc visits it gets freakin boring, and if nintendo were to brick my 25th anniversary zelda 3DS I'd be pretty irate. I own atleast 3 legit copies of Ocarina of time, two of the first two zelda games, and one of LTTP, so getting bricked over playing LTTP on my 3ds would be pretty crappy by far.