Arima : about the extra security checks, we can't know, it relies on informations provided by Apple. It's possible that they are going to give a new release (iOS6.1.1 or something like that) to patch the bugs of the 6.0.
About the AppStore, yes, they aren't making money on it, but they need to provide an "experience" to sell their hardware (since, after all, Apple is an hardware company), so yes, they won't release their grip on the AppStore.
But it's not because of the AppStore existence that HTML5 is lagging behind on their platform. It's because of the security department being behind every move of the other department, saying 'no' first about every new feature, and after that looking about what can be done to let a bit of that feature slip in the new iOS release <img src="smileys/smiley1.gif" border="0" align="middle" />.