A.David Utterback responds: The short answer is yes, you want to have a nail in every hole. It’s the shear and the withdrawl resistance of the nails that carry the structural load, and joist hangers are sized with a specific number of holes to carry specific load ranges. Typically, wider dimension members carry heavier loads, so deeper joist hangers have more holes in them for more nails.
Just as important is using the right type of nail. I can’t count the number of houses I’ve been to that have box nails, 8d galvanized nails, even roofing nails, instead of the common nails recommended by the manufacturer and required by code.
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