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this question can't be given a simple answer. All I can say is: it depends.
Many applications modules (root application modules) means you have many connections to the DB which might get you in trouble. This is also true for some transactional configurations you can use with task flows.
On the other side you may need the different application modules to have each region in it's own transaction.
I would advice to have a look at http://www.youtube.com/watch?v=toEuQvp73h8&feature=plcp which shown you some architectural patterns and when to use them.
And please always tell us which jdev version you are using.