No, Fortification discs do not double VP for locations.
You are misunderstanding the rules. When one of the ending conditions has been met, players total the points they have scored. Locations that you control score double the VP indicated on the map if you have a town disc instead of a village cube on the location to indicate control. The "If you have a disc in a location" phrase was in reference to "control" of the location which is indicated by a blue/red disc and not a fortification.
Each player now adds up the number of victory points he has. You score points as indicated for locations that you control, i.e. that you have a cube or disc in. If you have a disc in a location then you score double the number of points indicated.
You also score two points for each of your opponents cubes that you captured and four points for each disc you captured.
The player who has the highest total of victory points is the winner. In the case of a tie then the French player is the winner.
Under The Board section is a picture indicating that the hexagonal symbol with a number in it scores Victory Points at the end of the game. (Page 4 pdf, labeled page 2 IRL)
Victory points scored at the end of the game. You double the points if you have a town disc in the location.
Fortification discs do not indicate control of an area. What they do is explained on (page 3)
Fortify a location
To fortify a location you must play a fortification card and the location card for the location you wish to fortify. You must also pay three money to the bank. You then place a fortification disc under the cube or disc in the location. A location can only have one fortification disc in it. A fortified location starts a siege with an additional siege strength of two, and is also immune to raids. The number of fortification discs is a limit to the number of times this action can be selected. Note that if you had just resettled a location you could fortify it within the same turn.
Finally, under Starting the Game (page 6), they indicate how you control a location.
Each player starts with a number of cubes and discs on the board, which represent settled locations. Cubes represent villages and discs represent towns. Certain locations are already coloured red and blue, to indicate which side they are initially controlled by.
The British player should place one cube in each red square location and one disc in each red circular location. The French player should do likewise in each blue location. Having a cube or disc in a location indicates that you control it.