The problem is not that they aren't hidden - they already very much are.
It's that the upgrade didn't handle old posts that are already using tags that well, and I haven't found a tool yet that can mass upgrade the custom tags yet.
All that happened was BBCodes got reparsed, so yeah it should have gotten fixed that way.
All [thumb] ever did on phpBB's side was change the text into a HTML comment. It was up to the forum software to find this information to present in the topic listing.