The interior of the fictional Masyaf citadel in Assassin's Creed contains an extensive library, and the rear is a lush garden above a sheer drop. These two properties happen to be known features of the real Alamut, which was also a Hashashin fortress at this time. Subsequently, it is likely that the fictional Masyaf is a combination of features of both fortresses.

It may also be the case that the in-game character Al-Mualim ("teacher") is a portrayal of the real Rashid ad-Din Sinan, who was operating out of Masyaf at the time the game is set. Both characters are the leaders of the Masyaf citadel. In addition, both ad-Din Sinan and the fictional Al-Mualim die around the same point in time (e.g. 1192-4 compared to 1191). So there certainly are elements of the real Masyaf which have carried into the game, albeit modified. 

At any rate, a reference to Assassin's creed should only be made under the Popular Culture heading.