Only the literal top is different (frames are the same AFAIK). You can buy tops with zip out windows or without. Hell, you can still buy plastic windows.
The only major differences you'll find with zip out vs fold down windows are:
- if you install a roll bar. Some bars mate better with the zip out windows.
- rearward visibility. Zip outs get a larger window of viewing.
I have a zip out and prefer that. The reason is much to your point, actually. When I'm trying to out run a storm and fail, I can pull my top up & latch with one hand while going as fast as 30-35mph. Since the window zips out and the gaping hole is there, I don't have the drag that the full window would cause. Even in pouring rain, you're not going to get wet as long as you're moving.
It takes me about 4 seconds to unzip my window when the top is up and the car is in the garage. It really isn't a hassle.