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flo, the plugs are also called "bungs" and new ones should be available through woodworking or sailing catalogues and stores. Some folks prefer to get a plug-cutting drill bit and make their own, but I don't think that would be worth the bother for you.
Those voids definitely need to be cleaned out, all the way back to solid dry material, and filled. You can find articles on that archived at the West Systems (epoxy) aka Gougeon Brothers web site, they provide generous free advice and technical support to anyone who calls, even in the planning stage before you've bought anything from anyone.
You might want to look into deck coring problems a bit more before you get into the project, though. If you are lucky, it is only rotted/delaminting in a limited area, within some inches of the hatch. If the damage is more extensive--it can become a huge project. A tap hammer or a moisture meter are the usual tools to figure that out, although since you have access at the hatch, you might try simply ramming in a length of wire rod (heavy coat hangar) to see how far it penetrates, and how far back the damage goes.