I believe the X means it's an extra stage that you have to do certain requirements during another stage to unlock. Historical is the default story route and Hypothetical is an alternate "what-if" story line that can be unlocked.
X denote a branched route. If you fulfill certain conditions on a stage (you can tell by how there's a star) you unlock that branch .
Historical is basically the game following as close to the original history (as much as Dynasty Warriors can).
Hypothetical is a what-if scenario. As in what would happen if X kingdom have done things differently. For instance, the Wei hypothetical route has Wei winning Chi Bi and going onwards to conquering Wu and Shu instead of losing and ending the route at Fan Castle.
http://img202.imageshack.us/img202/841/be12546771e0f1be3d8f7d2.jpg Morning Rescue, official drink of Puella Magi!