I love the look of the shaker hood scoops on those classics. I wonder why they left those out in the newer models

Like all such scoops, its purpose is to increase performance at high speed by a 'ram air' effect, delivering high pressure air to the engine. Unfortunately engines draw air in hundreds of cubic feet per minute so scoops are not practical to raise intake pressures significantly. Other benefits of a shaker hood include elevation to prevent water from being drawn on flooded terrain, a cooler source of air, and a more direct path to the engine's throttle plate. Because of the high volume of air that engines draw, rain, even a downpour, cannot cause significant damage/wear to the engine.

I think the most recent stang with one was the 2004 Ford Mustang Mach 1