The bog-stock answer would be that something is messed-up, like maybe you had a mod enabled, and have reverted back to the stock game, or maybe added another mod. Either way, the first thing to try is to clear the Save folder, which is usually "C:\Users \UserName \Documents \SH4", unless you've used MultiSH4 and changed the name of it. Delete everything below that level. This will of course, take out all old Saves and the configuration files you have been using. The Save data though, is only good for the set-up you currently have. If after deleting those files from the Save folder and re-starting the game, you still don't have deck guns, then a re-install is in order, which would also include a deleting of the Save folder...
