First of all, it seems that you lost about four years of Opera's history and a lot has changed in that period. You can read the Desktop Blog starting from here to get your self a little more up to date.
Where's the bookmarks manager?
Ctrl + Shift + B or Menu > Bookmarks > Show all bookmarks
Where's the toolbar options?
There isn't one.
The help menu giving me a shortcut that doesn't work (CTRL-Click on toolbar) to access a settings menu that doesn't even seem to exist. (Settings: Toolbars)
This seems to be a help page for Opera Presto (Opera 12 and older) and is not valid for Opera Chromium (Opera 15 and newer).
Why did updating Opera remove features?
It didn't, you probably just installed the new Opera which never had such features. Your Opera Presto installation is probably still there.
Or for more practical help, how do I hide the text on my bookmarks tool-bar?
I'm not sure if it's possible.