If you can keep the hearthlings out of the storage room most of the time, then yeah that would have the intended effect. At the same time, I feel like my hearthlings would be in and out of there constantly – I’m an unashamed hoarder of virtual resources hahaha!. I also like to place storage in my workshops, and crates just fit/look better for that aesthetic IMO. The Dwarven kingdoms (when we get them) might have the skill and resources to use top-tier vaults in all their workshops, but most towns aren’t going to spend a lot of time making fancier storage items just as drop-off points to keep items near their workshop.
That said, I agree with your other points; it does fit. And yeah, it seems like the -1 won’t be a major impact. However, it means that decorating the workshop to overcome that -1 is both trivial, and pretty much mandatory. It feels a little off that we’re investing in making a significantly pretty workshop in order to overcome the minor penalty and have that minor positive as a result… it would make more sense to invest that prettiness in commonly visited spaces (town square, dining hall, etc.) Of course this all boils down to how much time is spent around the crates; and I suspect in most towns that will be less time than my hearthlings do.
The simplest solution, IMO, is to have “rough crates” (or just basic crates) as a level 1 craft, and then the fine crates have a neutral impact but obviously they’re a fair bit harder to get.
Alternatively, something along the lines of Finetems Mod or Home Sweet Home mod, where there are specific containers designed to fit into the hearthlings’ spaces, might solve this issue. It means more work on the dev team’s end, but might also encourage players to think in terms of “this building is an apothecary, this building is a mason’s workshop” etc. – any time you can inject story into the players’ choice of decoration/building/design is, IMO, a really good thing! In that case, crates would be a short-term solution or a quick way to box up and move several items at once, while the long-term storage would be the specially designed shelves/etc.