Anything is commonly considered organized when it looks like
everything has a correct order or placement. But it's only ultimately
organized if any element has no difference on time taken to find it.
In that sense, organizing can also be defined as to place different
objects in logical arrangement for better searching.
This is the definition of organized I go by :). So according to your question, I would broadly classify user behavior in two ways: Browsing, Searching.
Browsing: When user is not sure of what s/he wants, and is looking to discover items.
Searching: When user is looking for a specific item and looking for the fastest way to get there.
Now google has made the searching paradigm super popular and commonplace. So everyone is used to that. Flat lists work better with that, as it allows you to quickly spot the one item you are looking for from a list of potential matches.
Hierarchies are best for browsing, as it allows discovery of similar items.
Flat views a.k.a Index are best for quick search and resolution.
These both depend on the number of items as well. A flat list with over 10 items is difficult to comprehend at a glance.
In the modern times this question is moot as you can do both very efficiently and with little overhead.
My personal philosophy is organize hierarchically, to enable browsing (still a dominant mode of though when seeking with unknown objectives in mind), and generate a flat structure as an Index, or allow a search from anywhere.
Anyway context is very important so you need to give a better context to generate more concrete answers.