The Jedi Fortune Cookie "All warfare is based on deception" is from The Art of War written by 5th Century B.C. Chinese General and philosopher Sun Tzu.
Whilst undercover in this story arc, Obi-Wan uses the code name Ben; the name he will go on to use in the events of Star Wars IV: A New Hope.
The sign outside the building from which Rako Hardeen launches his sniper attack reads 'Noodle Bar' in Aurebesh. All the prison uniforms have the word 'prisoner' written on it's sleeve in Aurebesh lettering.
Rako Hardeen's helmet design is based on a rebel trooper concept originally designed for Return of the Jedi.
The 2020 anthology book "Star Wars The Clone Wars: Stories of Light and Dark" features a story based on all four parts of the "Rako Hardeen" arc that is told from Cad Bane's point of view. It is written by Tom Angleberger and titled "Bane's Story". The audio-book version is read by Clone Wars voice actor Corey Burton.