No offense, but so what if they could? I personally don't see why that's any reason to lock down the security of a rom hack of all things to the point where it inconveniences others who just want to play the game or transfer their saves. It's not like doing so would allow online cheating, it's just achievements.
At the end of the day, it is your project, and it's your call on how to handle the situation, but it seems silly to me to take something like that so seriously.
It sort of reminds me of how CTGP Revolution has strict anti-piracy, despite the game being out of print for like a decade and Wii disc drive failure being a thing. I get not wanting to encourage piracy, but you can't even legally buy the game anymore aside from secondhand sales, which Nintendo makes nothing from anyways.
. Saves on time, soap, water and money having to wash them. 
