There are a number of birds that can fly up to 10,000 feet. At 10,000 feet, the Shuttle is doing half the speed of sound. Hitting a bird at 10,000 feet would've been no picnic.

(In fact, the altitude record for birds is above 30,000 feet -- but these are unlikely to be found in Florida.)

Soyuz and Shenzhou both have a payload fairing that covers the entire spacecraft. Apollo had a partial shroud that covered the command module. These spacecraft do not even have an exposed heatshield during launch. Apollo didn't even need a fairing for aerodynamic reasons -- but it still had one anyway.