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Hi Guido,
pr2_arm_navigation/pr2_arm_navigation_config/config/joint_limits.yaml contains the actual velocity and acceleration limits that are used. If you are using the trajectory filter (which you will be if you are using the launch files in pr2_3dnav), it will use these values to determine the maximum velocities and set appropriate times for each waypoint in the trajectory so that these limits are always obeyed.
The "Moving the arm through a Cartesian pose trajectory" tutorial does not use the trajectory filter though. It assigns the times to each waypoint individually. It computes the time between waypoints assuming a linear segment between waypoints.
The behavior of the underlying joint trajectory controller is described here: http://www.ros.org/wiki/robot_mechanism_controllers/JointSplineTrajectoryController
Hope this helps,
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