If you check anything off with a yes on the medical, then yes, you will require a doctor's certificate approving you to dive. This is a standard that PADI if very particular about for safety reasons.
However, lots of smokers over 45 dive, so I doubt it would be a problem, but of course that's up to your doctor. If he/she gives you the ok, you can dive to the limit you are certified to, which is only 60 feet if you haven't done your advanced.
The form that I have specifies "if any of those items apply to you, we must request that you consult with a physician prior to participating in scuba diving". Perhaps your form is worded differently but there should still be directions and it should be clear...if you read the form carefully you should know what to do. Essentially, if you answer yes to any of the questions on the form you need to get a physicians clearance to dive.
Getting a doctors' certificate isn't hard. I downloaded the form, faxed it to my doctor and faxed it back the next morning, and then questioned me extensively all about diving and Couples on my next visit!