Yes! Your Hubway Annual Membership codes and day passes will still work with the Bluebikes system. The only difference is when you sign up using an old Hubway 24-hour code, you will get a free Explorer Pass (a 24-hour pass that gives you unlimited 2-hour rides). More about the Explorer Pass here.
If you're having trouble redeeming a Hubway gift certificate or 24-hour pass, email Customer Service at email@example.com.