I too have this issue. Clean Install of macOS Sierra 10.12 on a blank MacBook Pro. No third party apps like Kaspersky. All my individual bookmarks are present in Safari 10, and I have both a Favourites folder and a Bookmarks folder, each with lots of subfolders and bookmarks. But when I choose "Add Bookmark", the actual folder called Bookmarks is no longer available as an option in the "Add the page to" prompt. All the other subfolders (and Favourites folder) are. If I click Edit Bookmarks, Bookmarks and Favourites are there.
On my iPhone, I can see the Bookmark folder. So that says something..
On my Mac, I exported my Bookmarks.html file, and it shows a Bookmarks folder. So, it looks Safari 10 is mishandling or misreading the bookmarks.html file for some people.
Bug report 28487406 submitted successfully.