Yes, even though the channels do not meet the epoxy should penetrate from one to the other.
This is how I understand delamination. Hobies are made by a foam sandwich, meaning a layer of glass(bottom), a very thin layer of foam, then another layer of glass(deck) that is covered with gel cote. This method creates a strong, yet lightweight hull material. When delamination is present what has happened is that one or both of the layers of glass, for whatever reason, has lost it's bond with the foam. That is why it feels soft or sounds hollow/squishy. So when you inject the area with epoxy what you are essentially doing is re-bonding the loose glass layer(s) back to the foam. If there is delamination, there will be a "void" in the sandwich where the expoxy can penetrate.
Also, when you do the repair again, which I hope is successful, make sure you keep going back to your boat until the epoxy has cured. Sometimes, it will seem like the deck is full and you come back later to find that it will still accept epoxy, it's like it keeps sucking it up. Take a few cold beers with you or the beverage of your choice and just take your time with the repair. I literally spent hours doing mine. If you are in a warm climate, which I don't think is the case, just make sure not to leave the expoxy in the heat while you wait to see how well it took. Let us know how it goes. Like I said, I did my repair a while back and my deck is still hard as a rock after hard sailing (both lake and sea), and a steller pitchpole last weeked digging in the repaired hull. Too bad the insides of my boat are going soft too, but soon it will be time for a upgrade.

But I'm going to keep sailing her till she breaks I'm afraid.
I've said it before and want to say it again, If it weren't for the folks on this forum I wouldn't have had a clue what to do about my soft hulls. Thanks to Matt Miller for his postings and the rest of the hobie community for there support to novice sailors and ancient boat owners. Well, maybe not ancient but definately older than most products you can still get support for. What a company.