It's company specific. Nintendo and SEGA wisely know that allowing rom hacks to live continues to give popularity to their games, and might help encourage people to buy the games off of the virtual console.
On the other hand, Square Enix lives in the 90's and believes that if they terrorize people the hacks will go away.
Believe me, the current generation may have been cowed, but I bet you some day a new generation of hackers will simply figure out a way to add in plausible deniability to the rom patches.
At which point Square Enix can yell all they want.
That, and people in Russia can probably do whatever the heck they want
