At least according to Hyams's sequel.
Sometimes I figure the Monolith emitted the supersonic signal because it didn't want the astronauts to photograph it, or themselves in front of it. It's a strangely vague ending for the Floyd segment.
I thought it was a signal that humanity had advanced far enough to even find the Monolith in the first place. Thus it signaled to its creators that humanity was almost ready. Killing people would be counterproductive.
The Monolith clearly didn't care about being poked and prodded. In 2010
Dr. Floyd said that they tried everything - lasers, even nuclear detonators, and nothing worked. So the creators of the device had no problem with people poking around it. The Monolith emitted that signal because it was a 'trip-wire' due to go off whenever humanity found it. The signal was for the next phase in the plan, as it were (i.e. the transformation of Dave Bowman).