I like the idea, though bezier curves might be a little advanced for most users – and require experience and skill to operate.
Perhaps another option would be the ability to add mid-points to a link curve and drag the curve by the mid-point? For example, in OmniGraffle:
Note, that in this case, OmniGraffle considers the line to always extend from center of one figure to center of the other, and only displays the “visible” portion of the line. Perhaps this would make simpler the programmatic calculations needed when moving a note.
BTW, if you have OmniGraffle or similar, you can use figures like the one illustrated in the GIF as image adornments and take advantage of the graphics