There is no difference in meaning between the two forms.
The "If he hadn't.." form is a lot more likely to be used in spoken English and in informal written English. It is considered inappropriate to use short forms (hadn't, wouldn't) in formal written English, and this may be one of the reasons the other form is used in formal written English.
According to this NGram, up until 1970, "Had he not" dominated in written English, but written English has become progressively less formal over the years, and "Had he not" is now used rarely apart from in literary, period and formal writing.
Whether Clifford Beers would have made a name for himself had he not become mentally ill in 1900, or, given that, had he afterwards buried his psychiatric history and pursued his youthful goal of business success, is hard to say. Clifford W. Beers: Advocate for the Insane