Can a multimeter really accurately measure the output current of a SMPS?
Usually when we measure the output current to evaluate a DC power supply we are primarily interested in the DC component, and some mV or tens of mV of ripple on top (either from the power supply or because the load current has an AC component) on top of volts are not important at all. 

If you want to turn things around and actually measure the ripple voltage or current and ignore the 99% of DC component, you need something with sufficient bandwidth and sensitivity. Usually that would be an oscilloscope with some kind of a probe such as a current probe. Low-value shunt resistors are problematic at high frequencies since even a bit of parasitic inductance can greatly affect the voltage drop. For example a 5nH inductance will affect the reading across a 50m\$\Omega\$ resistor by 40%  at 1.6MHz.