your decking is spaced probably about 1/4 inch apart so the roof of the shed needs have a fall and be water proof.
I would just build a free standing shed under the deck with its own roof and not connected to the deck at all.
I would configure my roof joists at a down fall or front fall and deck it with ply wood and then tar paper it then shingle it.
I am not sure at all what your original question was pertaining to that was between the joists.
having your shed independant of the deck will eliminate the problems when your deck heaves and bows with the soil.
What do you think?
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