EnergyPlus has an object devoted specifically to modeling Air-Cooled IT equipment, and you can reference the input fields and output variables. To see how EnergyPlus calculates exit air dry bulb temperature, you can reference the Engineering document.
From looking at the EnergyPlus Engineering document, it does not appear that EnergyPlus performs calculations related to the thermal mass of the IT Equipment, since it doesn't request any dimensions or heat storage properties of the equipment.
If you have mathematical models to describe the server transient behavior, you can incorporate them into an EnergyPlus model using the Energy Management System capability. This allows the user to create their own variables and equations to apply various types of changes to the model. Usually, this capability is used in complicated control actions using logic, but I've seen it used to calculate air leakage connections between ducts / plenums and conditioned spaces (which EnergyPlus doesn't handle well).
