I'm here to actually ask about the same problem. Currently I'm using version 12 and I decided to try the new Opera 18.
With grinding teeth I decided to settle with the missing bookmarks and was about to start using it anyway, but then I found out that the ctrl + (1-9) aren't working.
Is there any plugin or any solution to this? I mean... there is plenty of other shortcuts and I don't see any reason why this one shouldn't work.
Thanks in advance,