Only a minimum number of modules are installed automatically in 4.4.0. If you go to the bottom of the Module Definitions page there should be more Core modules listed there that can be installed. I'm not sure if the Store module is there off the top of my head. If it isn't then it can be dowloaded from the Store project page. http://www.dotnetnuke.com/Default.aspx?tabid=891

I can't remember where I read it but some modules weren't included because they're being redesigned into another more improved module (I think Contacts was one of those). I think others weren't included because they aren't used that much as there are 3rd party modules that do a better job and people just ended up removing them from their install. I know I usually removed those you listed and those that the packages were included but not automatically installed (with the exception of the Repository). What you can do if you have a number of modules to install is put the install .zip files in the Install\Modules directory. Then if you go to the Module Definitions page they'll be listed at the bottom where you can check them and install them all in one shot.