This is not my area of expertise, Arai, so you should wait for other answers.
I would say that if a person named Zabriski is known for only one theory, "the Zabriski Theory" would be appropriate. If he or she is known for many theories, I would expect to see something like "Zabriski's Theory of Diminishing Returns at Casino Tables" for the first reference to the theory in an article, for example. After the first reference in the article it would seem perfectly fine to say "the Zabriski Theory" if you are referring only to that one specific theory. "Zabriski Theory", with no "the", would not look correct to me.
All that being said, Bibliolept is a source I inherently trust. Since he says that there is no difference or preference I'd tend to discount my expectations and wait for other answers to clarify the situation.
JamesM has given this a lot of thought, more than I did since my answer was predicated largely on my own experience or observations. I agree with his suggestions.
I would not use, to follow JamesM's example, the "Zabriski Theory," unless this was already in common use in the extant literature on the subject. In his own paper, the fictional Zabriski probably didn't call it the Zabriski Theory of X," but likely titled it only "Theory of X," Taking this into account, and as a matter of personal taste, I would be likelier to use the genitive of origin, writing of "Zabriski's Theory of X" rather than of the "Zabriski Theory of X."
Oddly enough, I would consider the opposite, to simplify things, if I were going to be speaking about multiple "Theories of X," each one presented by a different researcher. For reasons of expediency and to keep the text from being cluttered with apostrophe's, I would then say "Brasky Theory of X," "Zabriski Theory of X," and "Nixon Theory of X."
I suppose this all hinges on my anecdotally-derived belief that there are no rules governing this issue.