It's mainly a pre-plugin manager era thing that permits to prevent a plugin file from being loaded. For people that still install those files directly into
~/.vim/plugin, it still makes sense.
It could still make sense if you distribute a plugin (in the new sense:) made of several files that defines different things. But honestly, it'd be simpler in that case to have options that permits to fine tune what shall always be defined and/or how.
Note: it can also be used to check whether a plugin has been loaded (there exist other methods though), or to obtain the plugin version if we use that variable to store a version id instead of a boolean.
EDIT: Vim help describes another use case that makes a lot of sense (
Or the system administrator has dropped it in the system-wide plugin directory, but a user has his own plugin he wants to use. Then the user must have a chance to disable loading this specific plugin.