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O.K I was able to create a Joint trajectory point handler and it works fine (and reads the sequence number fine). As written here: http://wiki.ros.org/simple_message#Joint_Trajectory_Point_Message , there is a sequence number, so it was my mistake, sorry.

If someone gets stuck on it, this should be the start of the Joint trajectory point handler internalCB method

bool JointTrajPtHandler::internalCB(industrial::simple_message::SimpleMessage & in)
{
  bool rtn = false;
  JointTrajPtMessage joint_traj_point_msg;

  if (joint_traj_point_msg.init(in))
  {
     .....
  }
  ....
}