The phrase is being used here to refer to what is commonly called either Sophoclean irony or Dramatic irony, a literary device in which the reader knows something that the character does not -- something which is going to have a material effect on the character's future. This device is extremely useful as a way to build tension and to manipulate the reader's emotions, and therefore very important in literature.
The most easily recognizable form of Sophoclean irony is the horror movie in which the audience sees the killer hide in the attic, and then later the cheerleader and the quarterback sneak up to attic for a little extracurricular activity. The characters think they are going to get lucky. The audience know they they are going to get julienned.
Another example that springs to mind is from the Downton Abbey precursor Upstairs Downstairs in which we see beloved characters boarding a ship for America and in the final (season ending) shot, the camera pans round to the name of the ship: RMS Titanic.
So, the professor is giving lectures and entire seminars on Sophoclean irony, and yes, it is a big deal. Using the phrase "little did he know" is simply a way of simplifying a complex idea for an audience who mostly has no interest in literary theory. (Ironically, a case of the character knowing more than the reader does.)