“Do not pitch signal”

There are many reasons why an umpire might do this.  Typically, it is done  because there is conversation at home plate with the batter and/or catcher.  For example, a batter may have something in his eye, but doesn’t step out of the box, only asking the umpire for “time”.  A ball from the bullpen may have come onto the field.  A relief pitcher and catcher may have just run out of the dugout on their way to the bullpen, and the umpire is trying to protect them from being hit by a foul ball.

In your comment, if the pitcher is quick pitching, it is in violation of the spirit of fair play.  Why would you be concerned about protecting the defenses right to pickoff to first when they are the ones not abiding by the rules by quick pitching?  In extreme circumstances of a pitcher trying to continually quick pitch, it can be an umpire tool to hold up his hand creating a “time” situation rather than warn and eject the pitcher for violations of fair play.