I don't believe VFS for Git will ever be abandoned by Microsoft, but I'm doubtful it will ever get any more major improvements from them.
Scalar does use the VFS for Git client-server protocol, and both Scalar and VFS for Git rely on the same improvements to the git app itself, so I could imagine that GitHub would adopt the GVFS protocol and support Scalar without formally supporting GVFS itself.
[1] GitHub did announce future GVFS support in 2017 - https://venturebeat.com/2017/11/15/github-adopts-microsofts-... - but if anything came out of that I don't see it in GitHub help today.