Yes, there are some good reasons to use relatively short exposures instead of a single long one (with the total time, as you said, coming out the same).
First, you're right that avoiding saturating your sensor (aka, "blowing out your highlights") is one of them.
Another is that if anything were to go wrong during the single long exposure, image quality could be irreparablly damaged--imagine strong wind shaking your camera, or a neighbor accidentally shining a light toward your lens while photographing that dim galaxy you mentioned. Instead, if there are problems during one or some of your short exposures, you could just skip including those frames when you "stack" the images ("stacking" meaning to use software to glean all the data from the total exposure from the separate short-exposure images you shot). A great example would be leaving your camera's shutter open for an hour at night, to capture the night sky--"oops, an airplane flew across, leaving streaks from its lights!"--if you use 60 one-minute frames instead, you can just exclude the frame or two that captured the aircraft moving across, and use all the rest, like nothing happened.
Another important issue applies to astrophotography, which you tagged... As you may know, keeping stars' images sharp during long exposures requires a special, motorized mount that accurately tracks the moving night sky (it moves because of the Earth's rotation). If that mount's tracking isn't perfect, you'll get egg-shaped stars instead of round ones, and under worse conditions, significant streaking of the image. Poor polar alignment of the mount, improper balance causing stress on the tracking motors, and other factors can contribute to poor tracking--and one solution to working around these issues (if you can't resolve them directly) is to keep your exposures short!
