I don't know if it is actually Atom's issue, or there's something wrong on Solus side, but I didn't see any such GitHub issues posted on Atom's repo, so I decided to post it here first. 😅
So the issue is that atom no more highlights anything git-related, kinda fails to figure out that it actually works with a git repo. Meanwhile, I have rolled back my last Solus upgrade, so my atom is now v1.39.0 and git-related highlighting is back.
Also, I would like to report that I'm facing stability issues with Atom, for about a month by now. So when I click RMB anywhere inside Atom, it may randomly freeze the system, and I have to reset it.