No the ECM does not need re-flashing-----------unless you're adding a supercharger. Nor will he engine work harder with an air cleaner------except POSSIBLY at wide open throttle. At anything less than WOT, air flow is restricted by the combination of air intake restrictions and the throttle blade. For steady state conditions, removal of air intake restrictions leads to a slightly more closed throttle position and thus the same pumping "work" for the engine.
While the air may be cooler at the pickup point on a CAI, the difference as it the air enters the cylinder is minimal. Especially after the air passes through the intake system and manifold. Remember also that while 80 degree intake air may seem significantly cooler than 100 degree intake air, the absolute temperature difference (which is what enters in for thermodynamics) is 540 vs 560 degrees.
Have fun with your CAI and enjoy the extra noise. Your performance improvement will be unmeasurable except on the dyno (and then the difference will likely be within the tolerance band for the dyno) There will also be NO mpg improvements.
On the other hand, you will be shortening the life of your engine. Maybe like that of the air temp, it will also be meaningless. It doesn't matter to the guy that trades every 3 years if the engine wears out at 120,000 miles vs 200,000 miles. Of course, if you end up driving on a windy, dusty days, problems may occur sooner.
And don't expect Hyundai to warranty the guts of the engine if they see a K&N on it.
And there are some of us that won't buy a used car that has a K&N installed on it.