The website of Terminal Terrestre Guayaquil Fundación is sparse and in Spanish. There's a bit at the bottom saying 6:00 to 22:00, but in my experience different parts of a terminal open and close at different times. What are the opening times of the ticket vendors?
Post-travel answer for posterity: the bus terminal, including ticket offices, but excluding catering, is open and guarded at all times. The safest place seems to be the platform where the buses stop because only people with tickets can access it.