Same issue here. All .scn files show icon only no matter if new project created or older ones opened. It seems like the file type is assigned to Godot engine (also on my Mac) but a reassignement to XCode doesn't resolve the issue.
Xcode Version 10.1 (10B61)
My only solution was to uninstall Godot.
Allows Xcode to change 'Kind' file type.
Regarding the question, I have also seen the issue described with different versions of Xcode over the past 6 months or so, and did at one point, file a bug on it. With Xcode Version 10.2.1 (10E1001), I am not seeing it, though there are still other issues I see with the SceneKit Editor, which I have also reported. But they mostly go away if you just quit and reopen Xcode... For example, if you edit a .scn file referenced by a second .scn file, the changes to the first will not appear in the second unless you quit Xcode and reopen it - the second file does not refresh on its own, and just closing the tab for it and reopening it is not enough. It's this sort of minor annoyance rather than anything too troubling that remains to be addressed.
Without uninstalling Gogot Engine:
1) associate .scn to XCode again globally (CMD+i while selecting the scn file).
2) clean "open with" cache http://osxdaily.com/2013/01/22/fix-open-with-menu-mac-os-x/
3) wait until completed, in my case it fixed the association "temporarily" letting me to edit again scn files inside xcode. But when i tried to see file properties again(CMD+i) it reset it to Godot...