Wood screws coming out of the wood
I was afraid that might happen but it never has.  The wood is only ¼ inch and the short wood screws put some of the unthreaded shaft into the wood so there is less than ¼ inch to hold.  I run the wood screws through the wood with the points sticking out.  Then take it to the belt sander and take the points off until they are flush with the wood.  If they get hot they will burn the wood and then there is nothing for the threads to hold on to.  If that happens I throw the scrap of wood away and keep the shortened screw for the next piece. I usually take the screw back out put some glue on the threads and put it back in.  I like your idea of putting glue between the clip and the wood.
Mounting a straight shaft.
Put the clips on the paddle and hold it up against the side of the canoe.  Slide it around until you find a place where only the clips are touching the side of the canoe.  Mark that spot and glue the clips in.
The Bungidelebob in the bottom of the canoe runs through a plastic eye fastened down the same way as the clips. My empty 1 gallon water jug travels there.  Tie it down when I pack in the morning and remember to take it out at the last portage of the day.
MagicPaddler