there is a certain chance that they do different things, and "breaking" does not ignore 50% but maybe removes 50%...idk... a word from the devs to clarify things would be nice, but I guess we won't get that.

look at weapons that have one or the other, it is explained there:

- breaking: ignores 50% of armor

- piercing: ignores all armor

though this does not make sense for the psyker skill tree, as you unlock piercing (ignore all) before breaking (ignore 50%),
but then again, there are still a few little... "bugs" in the skill trees and also in other places ^^