Well, difference will create during minfication. If you don't follow the step1 , minification will break your code.
Uglify Version of your 1st code
myApp.controller("myAppController",["$scope",function(o){}])
Uglify Version of your 2nd code
myApp.controller("myAppController",function(o){})
If you follow step 1 , Angular will find definition of o
from injection.
But if you follow step 2 , Angular won't find definition of o
from any source.