Sorry, I know that you are not expecting an answer, but “it depends” :-) However, I think the best answer I can give you is what I did when I came across the same problem : I implemented a simple testbench to measure the time taken to perform certain operations on a huge superobject: I had average time measures for different levels of information entropy, and it turned out that the quickest solution was to restore the structure from raw materials. I specifically noticed this in Internet Explorer. It is possible that IE does not work well in loops (I reflect), and moving a superobject was rather slow than restoring it. Thus, this may not only depend on the structure of the superobject, but also on the javascript mechanism.
But, again, this is my business. I recommend implementing a simple test bench: it does not take too much time, but makes you get good results at the end; -)
EDIT
As an add-on, I wonder if there will be a creation of a super-object on the server side, and then send it back to the browser, since the JSON object will improve the results or not. I do not know if this is possible in your case. You can implement some kind of AJAX-accessible PHP script that receives commands (such as insert, delete, rename, whatever ..), and then it sends a new JSON object to the browser, which only the object will parse (maybe a quick operation? )
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