I managed to find a cause and a solution. I found that there is Debug mode that opens a section called Nimbus experiments. Apparently there is a switch there called "Simplify Homescreen New-users 145.0.1": if it's set to "Control", collections are back there. If it's on "treatment-a", they're gone. (You need to reload the browser for changes to take effect).

So it's some kind of experiment to change the interface, but I don't understand why there's no option to enable/disable Collections manually. I used this feature for bookmarks, it is so much more useful than Shortcuts because you can have more websites pinned. But without it, opening websites takes more time.