I doubt they will. The only thing that can really come out of this is more vampire/bat pony art and create a Vampirshy character. After all they did show at the very end remnants of fangs on Fluttershy so she still could be one.
It took a very different turn from what I was expecting. Still could not get over the fact they turned Fluttershy into a vampire (and based on that ending she might still technically be one). I thought it was gonna be a whole episode of them trying all kinds of different methods to stop the bats, stop the bats.
I'm going into wildlife management; sooner or later I'm going to have to explain to someone that wildlife may seem to harm them in the short run but will ultimately help in the long run.
As Aldo Leopold said, "To keep every cog and wheel is the first precaution of intelligent tinkering." We can't remove a species just because we think it's harmful to us; it might have a role in the ecosystem we never understood. The vampire fruit bats, for example, spread the apple seeds by spitting them. They were dispersal vectors for the apple trees, and according to Fluttershy the trees that grew from those seeds were healthier. Applejack only saw the ruined harvest.