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Most of the time I see shelving attached with the pocket holes underneath, which works fine for short bookcases. In the situation where you have floor to ceiling bookshelves where you can see the underside on the upper shelves is there any decrease in the weight bearing of the shelf if the pocket holes are on the top vs the bottom of the shelf?

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I would think if anything it would be stronger simply because of the angle that the screw would be going into the sidewall.
I dont think that you will have any problems. I recently made shelving for my garage (one long shelf, two feet below the rafters) with 3/4" plywood in which I used the Kreg Jig for pocket holes on the top to join 1"x 2" edge banding to the front. The shelf is 24" deep x 16 feet in length. I cut a 3/4"x1/2" dado for the edge band to give some support both in front & underneath. I spaced the holes every 8" with the Jig & step drill bit set @ 3/4". When I drove the first scew in, it came out a little through the face of the edge band. So I then reset the step drill to 1/2" & used the same 3/4" Jig setting & redrilled pocket holes again every 8" only this time they are set 2'' to the side of the first set of holes. The srcews hold the edge banding perfectly & do not protrude. Even with a bazillion hole in the leading edge & no plugs the shelving is now holding a LOT of weight. (wheels, tires, jet ski engines & spare parts, wood trim, boxes of stuff, & some wood working tools, etc.). The shelving is only supported with a metal "L" bracket every 4' & there is no bowing or warping yet. By the way, I did glue the edge band.

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