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Grammophobia has looked into it but has come to no clear conclusion. I thinks the extract is worth your attention anyway:

• The OED says the “cahoot” in the expression is “probably” from the French cahute, meaning a cabin or a poor hut. The French word, with the French meaning, was adopted into Scots English in the 16th century, but “cahute” was short-lived in English and is now labeled obsolete.

• The word (if indeed it’s the same one) reappeared as “cahoot” in early 19th-century America, where the phrase “in cahoot with” meant in partnership or in league with.

• The OED’s first citation for this sense comes from Chronicles of Pineville, a collection of sketches from the early 1800s about backwoods Georgia, by William T. Thompson: “I wouldn’t swar he wasn’t in cahoot with the devil.”

• The second quotation is from Samuel Kirkham’s English Grammar in Familiar Lectures (1829): “Hese in cohoot with me.” (Kirkham lists it among provincialisms to be avoided.)

• And the next, with the usual spelling, is from the Congressional Globe, predecessor of the Congressional Record. It’s from a speech delivered by an Ohio congressman, Alexander Duncan, on the floor of the House in February 1839:

• “Only think of this! A rank Abolition Whig from the North in ‘cahoot’ with a rank anti-Abolition Whig from the South.”

Grammarphobia looked into it but came to no clear conclusion. I think the extract is worth your attention anyway:

• The OED says the “cahoot” in the expression is “probably” from the French cahute, meaning a cabin or a poor hut. The French word, with the French meaning, was adopted into Scots English in the 16th century, but “cahute” was short-lived in English and is now labeled obsolete.

• The word (if indeed it’s the same one) reappeared as “cahoot” in early 19th-century America, where the phrase “in cahoot with” meant in partnership or in league with.

• The OED’s first citation for this sense comes from Chronicles of Pineville, a collection of sketches from the early 1800s about backwoods Georgia, by William T. Thompson: “I wouldn’t swar he wasn’t in cahoot with the devil.”

• The second quotation is from Samuel Kirkham’s English Grammar in Familiar Lectures (1829): “Hese in cohoot with me.” (Kirkham lists it among provincialisms to be avoided.)

• And the next, with the usual spelling, is from the Congressional Globe, predecessor of the Congressional Record. It’s from a speech delivered by an Ohio congressman, Alexander Duncan, on the floor of the House in February 1839:

• “Only think of this! A rank Abolition Whig from the North in ‘cahoot’ with a rank anti-Abolition Whig from the South.”

• The OED’s first citation for this sense comes from Chronicles of Pineville, a collection of sketches from the early 1800s about backwoods Georgia, by William T. Thompson: “I wouldn’t swar he wasn’t in cahoot with the devil.”

• The OED’s first citation for this sense comes from Chronicles of Pineville, a collection of sketches from the early 1800s about backwoods Georgia, by William T. Thompson: “I wouldn’t swar he wasn’t in cahoot with the devil.”

• Cahoot \Ca*hoot", n. [Perhaps fr. f. cohorte a company or band.] Partnership; league; as, to go in cahoot (or in cahoots) with a person. Usually used in the plural, and in modern usage often used to imply that the joint effort is unethical, shady, questionable, or illegal; as, a shill in cahoots with a pickpocket, to serve as a distraction. [Slang, southwestern U. S.] --Bartlett. [1913 Webster +PJC]

• Cahoot \Ca-hoot", n. [Perhaps fr. f. cohorte a company or band.] Partnership; league; as, to go in cahoot (or in cahoots) with a person. Usually used in the plural, and in modern usage often used to imply that the joint effort is unethical, shady, questionable, or illegal; as, a shill in cahoots with a pickpocket, to serve as a distraction. [Slang, southwestern U. S.] 
  --Bartlett. [1913 Webster +PJC]