'Co-' means 'together' or 'with'. This means that two 'co-directors' are on the same level as each other. If a company or project (such as a film) has two directors with equal responsibility, they are called 'co-directors'. They work together, and neither one is a higher or lower rank than the other.
A 'deputy' is usually a second-in-command, and of a lower rank. A deputy director would assist the director and do his/her job when he/she is absent, but would be answerable to the actual director. A deputy director has less responsibility than a director, and would be paid less.