They've done it before, and they don't seem to hate Sonic hackers or emulator authors for some reason. If you recall the SEGA Smash Pack games, those were modified versions of an old Genesis emulator called Kgen I believe, programmed by a guy called Steven Snake. Steven Snake is the author of the best Genesis emulator currently for PC, KEGA Fusion. It's nothing new for them to take freeware amateur work and use it for their own devices. I would assume because 1- they can't do any better, and 2- it's cheaper for them.
I doubt there was much in the area of threats to be honest. SEGA purposefully doesn't shut down a lot of Sonic hacking sites. There is one (won't name names, but it's the most popular Sonic hacking site out there) that claims to have a certain degree of "permission" to spread commercial rom hacks (not just the patch, the rom itself) around on their website. I don't fully believe they're telling the truth, but they're very open about it and SEGA does seem to not be bothered by their efforts unless they try to hack or distribute a newer Sonic game.
I doubt there was much in the area of threats to be honest. SEGA purposefully doesn't shut down a lot of Sonic hacking sites. There is one (won't name names, but it's the most popular Sonic hacking site out there) that claims to have a certain degree of "permission" to spread commercial rom hacks (not just the patch, the rom itself) around on their website. I don't fully believe they're telling the truth, but they're very open about it and SEGA does seem to not be bothered by their efforts unless they try to hack or distribute a newer Sonic game.