I am going to assume you mean that any request for
example.com/page.html outputs the content of the file from
websitedirectory/page.html. If it was "redirected" then the browser would show the subfolder in the URL.
In your case, there is no effect on SEO. Search engines will see the same URLs you see in your browser and won't know about the subdirectory unless you link directly to it.
One tiny thing to note: with your system it's likely that requesting the subdirectory page also works. In other words, loading
example.com/websitedirectory/page.html gives the same content as
example.com/page.html. This isn't an issue if no one knows about the subfolder (i.e. you don't link to it anywhere), but if the issue comes up it can be solved by using rel=canonical.
Incidentally, your site would be "physically" located at something like
/var/www/example.com/websitedirectory on the server. Your host probably has it set so your domain points to the folder
If you have full server access then you should set up the "virtual host" to point to the subfolder, as that makes things simpler for yourself (but still makes no difference for SEO).