In the HL model viewer you can change the subbody and skin of the model ( If it they have it ). How do I do that in Hammer? I can't see anything in the env_model ent to change the body of a chosen model...

Doesn't exist with the current Hammer.

But it must, what point is there to making submodels for the model if you can't use them?
Example of what I mean is opening HL mdl viewer and opening forts.mdl, going to body and changing submodel 1 to submodel 2.

You can use them, you just can't view them. Even with the beta Hammer you're lucky to see even the first body. Just remember that the # of the body in an env_model starts at "0" while in the model viewer it starts at "1" so subtract the HLMV body by 1 to get which number you should put in the env_model properties.