If the deck is cored with plywood and you are only replacing some core I would stick with plywood. For a total recore I would switch to balsa.
At the edges where the core tapers I would shape the plywood for a close fit and the thickened epoxy will fill in the gaps. If it is not shaped to fit you will use more epoxy and plywood is less expensive than epoxy.
I wouldn't worry about hard spots. Many manufacturers replace core with solid glass for hardware attachment. As long as the skin is strong enough it is not an issue.
Here's a link to a recoring project on Glissando, Tim Lackey's own boat. A lot of good information from an expert at this - he restores boats for a living and does a great job.
Pearson Triton #381 Glissando | Deck Recore Project