Last week, we ran a post promoting "messy organisation", where you consciously don't organise stuff in order to be more efficient. I'd argue there's a kernel of usefulness in that notion, but that calling it "being messy" is not the right way to view it. It's a question of not being more organised than you need to be.
The example we cited from a post on the Productivity 501 blog talked about how putting all your cutlery into a drawer unsorted might represent a better use of your time than carefully sorting it into sections, since it doesn't take that long to pull out the items you need regardless. Reader Gus also offered an even better example of where it makes sense:
In my home office, bank statements are all filed away together, not organised one little bit. I never have to get them out, so there is no point.
The key is that it depends on how often you use the items. It's dangerous to extrapolate that concept to all areas, because it doesn't always apply.
Sticking in the kitchen, while it's pretty easy to sort cutlery (it's all about the same size), a cupboard filled with storage containers can rapidly become a messy pile of unsortable junk and unfindable lids if you don't put some effort into sorting it. More generally, it can be a very short jump indeed from "It doesn't matter where in this drawer I put this stuff" to "it doesn't matter where I put this stuff, period". Making a conscious decision about what needs organising is always wise, but it needs to be on a case-by-case basis.