First and foremost, Flathead is now fully open sourced. Don’t worry about purchasing the plugin there.
You can build your entire game using flathead, though not in its current incarnation. The API was split off of UE4 and needs to be rebuilt. If there is more interest in this I would love to hear about it so I can prioritize my time accordingly.
Not sure what you mean by it affecting your game. If you are referring to performance or stability, not likely. The JS engine behind Flathead is the same as the engine behind Chrome and is quite fast and stable. Though, it should be noted that the same issues you would run into on this front in C++ apply - build good algorithms, optimize your implementations and try to avoid doing bad things and your application will be grand.
There are currently 11 games being developed using Flathead as its core, some GUI tools and I am using it at work to drive some of our other systems that need a scripting binding. I wont speak for them, but my own experiences have been positive.
What are your goals or dreams for using JS to drive UE4?
Read More Here: GitHub - OpenGneu/Flathead: This library is responsible for encapsulating the V8 Libraries and providing the interface to be used by Unreal or any other platform, really.