I'm not too concerned about storage, but I'm curious about how others are approaching this. I'm more than happy not to hack into that bookmatched deck just so the kiddos can stow a water bottle...

Patrick:
Are you installing bulkheads? It's necessary (IMO, and certainly traditional- for ventilation/pumping) to have access of some kind into any compartment, so you'll need at least an inspection plate for that.
Some boats have a 'swing up' backband - built on a UHMW or nylon sheet, fastened with one bolt on each side to the cheek plates. Those allow access through the back bulkhead, though you may have problems retrieving items that find their way farther aft.

One of my paddling friends has a 8"/10" inspection plate in the front bulkhead and he loads gear through that. When he's beachcombing for interesting driftwood, he can get some long 'finds' into the boat once that inspection plate is removed!