Overprint Preview is not turned on by default in any version of InDesign I've ever used. You simply toggle it with a keystroke (Cmd-Option-Shift-Y on Mac, Ctrl-Alt-Shift-Y in Windows) or choose from rhe View menu.
What boxes are you referring to? Please show us a screen capture of what you're seeing (perhaps I'm misunderstanding you).
Are you sure that you're talking about Overprint Preview which needs to be turned on under the View Menu when a document is open? This option is Grayed out when no document is active so it can't be set as a preference. It sounds to me like you're talking about Hide/Show Frame Edges which can be set as a preference by choosing to either hide or show the edges of unstroked frames. To make sure that you don't have all those "annoying boxes" as the default go through the View Menu>Extras>Hide Frame Edges. Do this with no document open and then quit the program. When you relaunch InDesign the annoying boxes will not be there anymore.