An omake is a short story sometimes related to the main plot, but does not have any bearing on the story. They are usually used purely for comedic purposes. If you don't read an omake chapter or watch an omake episode, then you'll still be able to to understand what is going on.
EXEPTION: Some of One Piece's cover story arcs do have a direct impact on the main story: Buggy and Alvida teaming up to kill Luffy Hachan meeting and saving Camie Koby and Helmeppo joining the Marines under Garp Mr. 1, 2, and 3 along with Sir Crocodile going to Impel Down Ace searching for Blackbeard
Other than this example Omakes do not influence the main plot.