I would like it very much, if you could actually upgrade the shops and warehouses (in addition to possibly already existing storage space), which would also change the look of the interior in a very immersive way.
Give the buildings a realistic amount of slots based on their size and designated use, a flag what kind of storage those buildings can store (no wardrobe for example), and possibly even "unlock" (in a form of progress stages maybe) generic clutter that only have a visual purpose to make the building look used (tools, brooms, buckets, rope, etc)
If the player drops a container in the inventory of the building, it upgrades the maximum storage space (Not sure if it should maximise the global storage space, or just make the containers usable. I could see problems with the first option if containers are being removed, etc), and shows the container in-game.
This would allow for a very neat progression/development process. Example: You start off with an empty warehouse, and the warehouse grows with the growth of your business/village in a very natural way. In the end you have a packed, lively warehouse, filled with barrels, crates, all sorts of containers, clutter.
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If you want to go even further you could also make warehouse upgradable. You got the default warehouse, and then you got "specialised" warehouses. A specialisation will result in different looks, and different container slots. A storage unit used to store wood will behave differently from a unit that stores other materials. A unit that stores liquids will behave differently from a unit that stores food/game meat/etc.
Of course this sounds very ambitious, but I think the game would benefit in the long run. You already need to build loads of warehouses now, if you get to certain point (which probably could be handled with rising the capacity internally), which can result in a very inhomogeneous looking area if you do it wrong. Even more if you think about the future of LiF, the MMO, potentially huge cities, with harbours and warehouse districts.