It is a good thing to make repairs to your home as a well maintained home will show and possibly sell for more money in any market. A lot of questions need to be answered before you can go much further. First of all, you mention the deck and then the roof, is it a covered porch or is he referring to the roof of the home?
Before you go any further you need to get at least one if not more additional opinions from licensed contractords. Don't tell the next contractor anything about the opinion of the first because you want to hear it from them that there is a problem. After they render their opinion and they say nothing about the roof then you could introduce the topic of the roof and have a discussion then, but not before. Compare what they say to the first contractor and then make a decision.
I don't know how long you have owned the home, but did you have a home inspection performed by an ASHI certified inspector? In his report did he note any issues with the decks or roofing? If he did, did you receive compensation from the seller for repairs that you would have to perform? Is the deck an add-on to the house and if so, was it done by a licensed contractor using permits? If it was, then it should have been inspected by a city/county building inspector in your area. This usually guarantees compliance, but not always. Did the previous homeowner add this to the house and if so, did they disclose this on the "Seller's Disclosure"? If they had the work done or did it themselves but did not disclose it to you, then you make have a case for recovering the expense of that additional repair. You are doing the right thing in contacting your agent and I hope they can give you some of the necessary answers.
You need to get as much information in front of you to be able to make the right decision. One thing to think about is if you are replacing the wood on the deck and if you can afford it, you may want to replace all of it using material made from wood fiber and plastic such as TREX. It is very low maintenance and will last a lot longer than wood. It may cost a little more for the material but you will save money in the long run in your cost of maintenance.