This can all be controlled by a Preference. Below is for Mountain Lion, which was changed slightly from Lion:

1. Apple Menu - System Preferences...

2. General Preferences

3. Select "Close Windows when quitting an Application" - this makes it so windows dont open when you reopen an app.

4. Now when you shutdown (and tell it not to reopen windows on restart) they will not open then - or later.

This can all be controlled by a Preference. Below is for Mountain Lion, which was changed slightly from Lion:

1. Apple Menu - System Preferences
2. General (under Personal section)
3. Select "Close Windows when quitting an Application" - this makes it so windows don't open when you reopen an app.
4. Now when you shut down (and tell it not to reopen windows on restart) they will not open then - or later.