I’m also experiencing this. It pollutes the output of my build script and prevents me from seeing the output that matters.
I’ve tried to fix the issue with no avail. Check the ticket here and discussion here: 
August 2, 2019 11:36 PM as reference.
Also, there’s a related discussion (to js-kit and Haxe js externs in general) here. Your input is welcome.
Lastly, It’d be nice also if Haxe had a way to suppress all warnings. If the Haxe gods are hearing me, please add that option!