These days the most common attacks against computer systems are targeted at the application layer. Often these attacks gain access to system resources by exploiting buffer overflows in the applications or by gaining elevated privileges by executing code with inappropriate checking.

These types of attacks are not bound to any underlying network protocol, so we can not expect any changes if we are deploying IPv6. The operators of the services, must be aware of the problems, and update their systems to prevent such an attacks to happen.