I think the big thing with the Borg does not overuse them, they are way scarier when used sparingly, if they show up all the time, they start becoming generic villains and lose their menace.Thinking about my first Star Trek experience. First Contact was the first movie I saw as a little kid in the 90s and this scene scared the tar out of me:
Star Trek would probably have to be adapted to be kid friendly as I don't know how scary they are allowed to be. We still don't know the time period it will be set in. If it's the TNG era, I wonder how they'll adapt the borg. That clip admittedly is pretty mild in the scare factor compared to other scenes.
I do think you can do the Borg in a kid-friendly setting, the Borg are sinister, but they are not villains who are too dark to work on a kids cartoon, Borg stories are not overly gory, their horror is somewhat more subtle.