Will there ever be items or weapons found exclusively through looting, i.e. you can't buy them in stores?

So that is absolutely a yes. I think it was on one of the recent ISCs with Samuel Molina, who mentioned that, yes, for 3.17, we're introducing for the first time different rarity levels of items and loot boxes. So yes, some of those rare items will not be found in stores and they will be hard to get, proportional to their value.