There are a few games on iOS/Android that have been made in C2 using wrappers, so no, it's not a problem. It won't be rejected because of that.
You'll only have to care about cocoon/appmobi costs if you really sell a lot, and let's face it, if you have a game that is really successful to actually make some decent money, you'll probably should think about opening your own company and actually getting licences for cocoon/appmobi.
About support for your games, if you have a problem, you should take it directly to cocoon/appmobi. They also have forums, people who help, and etc. You may not be able to mess with your code properly by using these wrappers, but if you ask for help in their websites, they will help you.