This is really what it comes down to. My cyclocross commuter is a bike with drop bars, but the bars are much closer to the saddle height than my road bike. Since the handlebars are higher on my commuter, riding in the drops isn't uncomfortable at all - but I still do spend most of the time in the hoods. Riding in the drops on my road bike is more aerodynamic than my commuter since I'm lower, but I do have to focus on my posture more.

I love handlebars with drops because there are so many choices for hand positions, and with the cyclocross brake levers on the tops you can brake from anywhere. If you don't like them low you can always just get them higher relative to the saddle height by picking the right frame - the same goes with any kinds of handlebars