Only the first of the above suggestions stands up to scrutiny by virtue of the age of the phrase. The earliest references to hooks and crooks in this context date back to the 14th century - the first known being from John Gower's Confessio Amantis, 1390:
What with hepe [hook] and what with croke [crook] they [by false Witness and Perjury] make her maister ofte winne.
Gower didn't use the modern 'by hook or by crook' version of the phrase, but it is clear that he was using the reference to hooks and crooks in the same sense that we do now.