Yes. The expected PUE and actual PUE of your data center both account for associated cooling energy.
Power Usage Effectiveness (PUE) is a standard measure of facility infrastructure efficiency in the IT industry. It is equal to the total energy consumption of a Data Center (for all fuels) divided by the energy consumption used for the IT equipment. That is: PUE = Total Facility Source Energy/ IT Source Energy.
The energy consumption associated with a Data Center’s cooling requirements would be included in the Total Facility Source Energy value, hence included within the PUE metric. A rating is generated by comparing an expected (estimated through statistical regression analysis) PUE to your data center's actual, entered PUE.
More information on how to properly benchmark your Data Center: