Your Applications folder doesn't reside in your home folder, it resides at the root level of the directory.
Some apps will place an Applications folder in your home folder, but it's not the same as your /Applications folder. It will contain a small set of programs at most, usually placed there by well-meaning but misguided developers that think that's where applications should go. I wouldn't recreate it unless you absolutely need it. If you need it, just make a new folder there and name it Applications. It won't contain all of your Applications (since they are in /Applications), but you can store apps only for your user account if you really want.
jW