It is normal for your installation to run slower right after the prebinding has been done : its speed should greatly increase once the applications have been launched once.
Also, it is important to restart right after you have performed the pre-binding and not to use the computer while it is running.
Updating the predinding is probably the most intensive task listed on this page and, as suggested, should mainly be seen as a remedy for sluggishness. Performing it on already speedy installations will not damage them but you probably won't experience a terrific speed boost.
Also, be sure to run it on a "healthy" installation : the other maintenance tasks should be performed first.