Modeling Evaporative cooling systems (ambiator)

The amount of fresh air for a zone must be equal in both baseline and design case models. Typically, for DOAS, it means zones get a little more air than is usually nessesary as per minimum fresh air requirements such as ASHRAE 62.1. This is okay. The baseline VAV system must bring the same amount of fresh air into the zone as the DOAS. It is a requirement of 90.1 App. G.

Why are the proposed model's capacities not enough to meet the setpoint? Either your capacity is too small or your setpoints are not right. A narritive would have to be pretty convincing as to why your case should be handled different.

In a similar climate, Tucson, AZ, evaporative cooling also exceeds unmet load hours on an annual basis. Management and workers accomodate this with more breaks, earlier working hours, shorter days during the hottest season, as we have done for decades, but ASHRAE and LEED allow no exceptions. It is still the most efficient cooling system for a hot, dry climate. We just can't prove it with the existing criteria.

Joyce described schedule adjustments managers and workers make to avoid the hottest part of the day (I just moved to Phoenix, so I understand!). It would definitely require more effort, but close attention to your thermostat and occupancy schedules may help with unmet hours in the situation you describe. If you adjust your occupancy schedules (for proposed and baseline) to reflect the actual building occupancy, such as 6 am-3pm, or with shorter days in the hottest part of the summer, and then schedule the unoccupied hours at a higher setpoint temperature (this part is very important!), you may be able to mitigate the unmet hours in the situation you describe. Also, someone please correct me if I'm wrong, but I don't know of any requirement within the mandatory requirements of 90.1 or Appendix G that require specific thermostat setpoint temperatures. Ensuring your space setpoint in the model reflects the actual operational setpoint, which tends to be higher in our climate than in cooler areas, would also be a good thing to check.
I haven't modeled evaporative cooling for a LEED project, so I can't speak specifically to that technology. Best of luck!

We are modeling a factory, there will be no HVAC system only heating and ventilation, the thing is that the ventilation will be supplied by a direct evaporative cooling. Can we assume the proposed system to be Heated only?

You must model the proposed as designed so it must include the evaporative cooling system.