I don’t preserve certain settings on purpose because they have a tendency to confuse less experienced (or less frequent) users. For example, filters are discarded when you restart the app. That’s because people sometimes filter their images, forget and then wonder “where did all the images go?”. This is very understandable, especially if they aren’t using the app every day. With Show Subfolders, it’s similar. It is a common behavior for people, when faced with an app doing something they don’t want, to quit and reopen hoping the “bug” goes away, even though there is no bug. So, if they have turned on subfolders and pick something large, like their hard disk or a network share, then the app will spin for a while. Quitting and reopening will just start over again, which is very frustrating.
So, the short answer is maybe. I figure that avoiding this problem for inexperienced users is a good trade off vs. the annoyance of having to pick the button each time to turn it back on.