You both may get additional answers by posting your questions to the
LEEDuser.com since these are mostly LEED questions.

For the nat. ventilation question: Is there any mechanical equipment at
all in the building? It is my understanding that you can model the HVAC
that you have in order to submit to LEED. If not, I think you'll need to
share more information about the building's geometry to get an answer.
Being registered as a LEED project means nothing as far as it qualifying
as an eligible project. Also, you can't model operable openings that
don't exist. Sorry!

For the cold rooms question: refrigeration is a process load and all
process loads must be modeled the same in the baseline and proposed
cases, unfortunately. The only advantage you get from more efficient
process loads is less "noise" in the overall model which helps in your
overall percentage of energy savings.