It is theoretically possible to increase the cap, it's something I'm still contemplating along with possibly rebalancing some of the requirements by lowering some numbers.
I'm going to be adding Tier 2 materials soon so I will likely decrease the number of items required to craft armours/weapons and see how that goes before I really decide on whether I should try increasing the stack number.
Storage on the other hand is not very likely but it's also something I'm contemplating. I'm not sure how feasible it would be to make a storage that can store everything but some sort of specialised storages might be possible.