When it comes to pin bones, I'm a puller/plucker rather than a cutter. Generally don't pull them before vaccuum-packing fresh fish.... if you are worried about a puncture, just pack the pieces flesh sides together and skin sides out. That way only slime and scales against the vac bags.

On smoked fish, I always pull the pin bones prior to vac-packing since they tend to become very exposed as the meat shrinks.