There are many factors that will change the performance of the engine. Altitude, air temperature, and humidity are big factors that will affect how an engine will run. Air density increases as air gets colder. This means that there are more oxygen molecules in the same space when the air is cold. When the temperature drops, the engine will run leaner and more fuel will have to be added to compensate. When the air temperature gets warmer, the engine will run richer and less fuel will be needed. An engine that is jetted at warmer temps may run poorly when the temperature is colder and vice verus.
The bike will actually run better up top with a little extra oxygen. However you do want to be careful at freezing temps.The Ninja 250 is susceptible to carb icing in certain conditions. For the Ninja 250, it appears that the range of about 20° F to 50° F (-7° C to +10° C) with visible moisture (fog or rain) can cause carb ice. Pod air filters may exacerbate the problem, since they can allow more moisture into the carbs than the stock airbox.