Those are not decoupling capacitors. They are there precisely to do what you see on the scope - convert square wave into short pulses. This circuit specifically toggles on the negative edge of the square wave.
Normally the toggle voltage is kept at 1/2 VCC by the resistive divider. When the negative edge happens, it shortly pulls the cathodes of the diodes low, those toggling the flip flop.
But yes, it is better to specify what capacitors you are talking about. Because the ones shown at that link are only necessary before the flip flops. Logic gates should have stable levels, which is shown on the FIGURE 6.