It's doing what's called prebinding, a process kind of peculiar to OS X. The installer runs this little program that looks for all the library functions used by your programs, and it makes up a little table of where to find them so that the program doesn't have to look them up every time it starts.
When you put on system updates, there are usually shared libraries in there, so the same kind of thing has to happen. This time it finds all the other programs that use the new libraries and fixes up their tables to match.
In other words, it's not really optimizing the disk in the way people usually understad it.