Many notifications have been disabled because a lot of emails were being sent by the site that people were just marking 'spam' (because they couldn't be arsed to turn them of), which resulted in us getting blacklisted in a bunch of places.
I'm afraid that the questions and status update notifications may have been a casualty of this change.
Is the problem with them appearing on the site/in your feed (i.e. at the top right) or were you specifically looking to get an email?