I’ve never flown into the Guayaquil airport, but from what I’ve found online it appears there are luggage storage options. According to http://www.sleepinginairports.net there are luggage storage and lockers located in the arrivals hall and available 24 hours a day. A traveler on the lonely planet forum states that there is a company which provides luggage storage located just outside of the International arrivals area on the ground floor.