Is taking money from the restaurant daily to meet one's needs, after agreeing to defer the salary, considered theft, and how can one atone for this without being able to inform the restaurant owner?

If you agreed with the restaurant owner on a deferred salary after the restaurant's success, then you must fulfill the agreement unless you are harmed. Taking a salary without his knowledge is a breach of trust. If what you took does not exceed your right, you are not required to return it, and you may demand the remainder.

However, if the agreement was to work for free until the restaurant succeeded, then what you took is theft. You must repent and return the money or seek absolution from its owner. If you fear corruption, then deliver the money to him through indirect means.