The short answer is: the Privacy Protection Act requires a subpoena because it allows the target of the search to assert their first amendment right, which matters in America.
You can make your assumptions about the existence of stolen property and who knew what when as part of a conversation among friends, but those assumptions don't mean anything in court. Your reasoning mixes all sorts of different issues (trade secret law, theft offense, intent) that would result in lots of folks going to jail, if the law was so imprecise; it's not.
You may be right about this. I am not an attorney but I could see two possible arguments that a warrant is valid rather than a subpoena in this case.
1. "The Privacy Protection Act goes even further. In most cases, it requires police to use subpoenas, rather than search warrants, to search the premises of journalists who are not themselves suspects in the offense that is the subject of the search."
http://www.mcguirewoods.com/news-resources/publications/media.0101.pdf
In this case, Chen may be the subject of the search to find corroborating evidence of purchasing stolen property or breaking trade secret laws.
2. Chen works for a Blog (website), and Blogs may not be part of the protected class (journalists) that Privacy Protection Act protects because Bloggers are not an explicitly named member of the class.