Depends on the model.
For the F-15C and D models, the CFTs can be selected (they are part of the LOD, but can be selected in the loadout screen). For the other models that have them (E model and later) they are part of the model and cannot be unselected. In the case of the SE and R models, loadouts will have to proceed a bit differently due to the internal CFT bays (details pending).
For those who are unsure here...each model you see in the screenshot is a different LOD. There are physical differences between each aircraft requiring a different LOD (exception being the Japanese Eagles which use the C and D LODs, the CFTs have simply been removed via a data.ini edit). There is actually a C model that the Saudi's use, but since it doesn't even have a different designation, it just uses a Saudi skin and gets an entry in the USERLIST for the C model.
FC