Hmm, I've used shear pins in rockets from 38mm to 7.5", from H to N motors in cardboard, phenolic tubing, and fiberglassed paper and phenolic. In most tubes the shear pins are just below the top of the body tube. I was taught you want the shear pins close the the end of the body tube so the broken pins don't drag over a long area and possibly bind. I've never had any real damage to a body tube other than the hole deforming on plain paper tubes. But that can be minimized by soaking the area with thin CA.
I use the typical nylon screws (2-56 nylon) with larger rocket and styrene rod with smaller ones. I don't think I've ever seen a tube damaged by a shear pin as described by soopirV. It would be interesting to hear more details.
When you think about it the strength of a shear pin should be far less that that of a body tube. I think if it were a bigger issue we'd hear from a lot more folks with damaged body tubes. I'm not saying it can't happen but in the 15 years I've been flying (and helping out at launches) I've never seen it.
Here's a simple test you can try: drill your holes, insert your shear pins, and pull sharply on the nosecone to break the pins. My experience is that you'll get a clean break of the pins with no damage to the tube at all. If the holes do get damaged you can just fill them and drill new ones.
But obviously my experience differs from soopirV, so as always, your mileage may vary.
Tony