There is an increasing number of articles appearing in mainly European news magazines highlighting the difficulty (or virtual impossibility) of monitoring calls made via Skype.
Mainly Drug Enforcement Agencies are facing problems in listening in on calls between dealers, who quite openly instruct each other to switch to Skype to continue conversations.
The main issue seems to be that no one to date has been able to reverse engineer Skype's software in order to figure out a way of eavesdropping.
Perhaps this is the true reason behind the ban on VOIP in the UAE?