It seems to be a mixed result.
I have Water in Medieval Engineers mod, and that appears normally.
But I specifically added the Dirt to Clay mod listed in your screenshot (top item), and can see the issue with it.

From my own experience this is more likely to happen with more items on the list. Also it is almost guaranteed to happen when sharing the save file with someone directly (through pasting someone else's save folder into your own)

Reproducible when you manually copy worlds into your savegame folder. At least this is what I usually see, when I import a server world to my client.
Not sure if this also applies to worlds that you loaded from the workshop.

I did not load a world from the workshop This was a new game started after ME:CE

I found the issue.
This happens if the world has any mods listed that the user is not subscribed to. You'll know which ones you aren't subscribed to, as those are the only ones that appear normally.

This was an old bug that was always there, but I think the multithreaded changes made in CE caused this to surface.

This has been resolved and is scheduled for the next hotfix.