Hack dev here. I reviewed the ST3 changelog and it appears that there were changes in whitespace rendering that occurred in builds 3132 and 3133.
I am more than willing to work on changes on our end that might help here, but I don't know where to start unless someone can provide details on the changes that might have introduced issues with Hack rendering of whitespaces or glyphs that are being used to represent them in the affected builds.
Will keep an eye on our issue report submitted by @xdefrang for any updates as you discuss this here. Thanks!