Nevra,
I don't know of any thesis specifically on museum architecture off the top of my head, but the New York State Historical Association Library holds all the Cooperstown Graduate Program theses. The NYSHA library's collection is not on-line, but they do have a website: http://www.nysha.org/research.htm#resources. The librarians are very helpful, and you should not overlook this valuable resource.
Good luck!
-Janna
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