No. The game itself creates piles of stuff all the time. For instance, when you kill goblin ambushers at your entrance using large, serrated steel discs, the game just stacks their stuff one on top of the other. But there's plenty of other times...
Your dwarves will fill any space in a stockpile even with an empty barrel on that space, so long as the stockpile isn't furniture. I've seen 8 empty barrels in the same spot as a newly hauled drink barrel in the booze stockpile.
Bins can store quivers which can be actively storing arrows.
Cabinets and coffers can hold items which themselves are holding items.
It only seems like an exploit because our dwarves cannot stack multiple objects in stockpile ON PURPOSE. They'll do it just fine on accident. The dwarves need SHELVES to allow them to store multiple items (including bins) in the same tile on purpose. Build a shelf (out of all suitable materials: wood, stone, metal, clay, glass, etc), install it in a room to allow it's owner to use it, and let it as barrels and bins by the stockpile system. When a stockpile is full, a dwarf grabs an unused shelf, carries it to the stockpile, and places the object that was in that place (whether its a bin or a barrel or door or statue or whatever), and goes about their business.
This would create the following cascade:
item -> bin/barrel/jar/pot -> shelf
Bags would fill up a barrel, and barrels of bags would pile up on shelves.
The real problem would be FPS loss as we would have this added layer of containers to be search through.