Turning the repair into a rooftop deck - to answer this question its important to know what type of roof you have: steep gable, hip and valley, flat etc. Building a rooftop deck requires a fair amount of engineering to ensure it is stable enough to support guests. This might include a partial demo of your existing roof structure to install the standard joists needed for decking - all of this requires design approval from your local municipality and inspections to ensure its built to code.
So on the surface I would tell you building a rooftop deck is quite the undertaking and might be more expensive that you're thinking.
As far as which questions to ask the roofing contractor, I would just make sure they're removing the existing damaged/old roof before they replace it. Sometime when I work on residential homes I see roofs that have several layers of roofing - not only does this get heavy, but also decreases the effectiveness of your new roof. As long as you're going with a reputable roofing contractor, they will know all of these things. Also important that your drip edge flashing is either in good enough condition to be kept, or completely replaced with the proper galvanized material. Again, as long as you've hired a reputable and trusted contractor, all of these things are pretty standard when replacing a roof, its your roof deck conversion project that gives me qualms - design/permitting/scope of work can be intense.