Spent more time working with it today. I've observed a few differences so far. First, the 1616 has a master output level knob and meters on the front panel. But both are only active when the signal is going to the analog outs. With the signal going to the digital outs, you no longer have a knob you can quickly grab to turn everything up or down.
The master out fader in Sonar still works to control output level. But you can't always grab that in a hurry if something loud and horrible suddenly happens.
The other thing I'm noticing is the output seems louder overall. I normally kept the output knob on the 1616 all the way up or nearly so. But it seems I must have had the input attenuation set a little low on the EQ because the signal going through the the digital bus seems about 2-3 dB louder.
Actual sound quality is the same as far as I can tell. I'm going to continue to experiment for now and see if there are any other differences.
If nothing else, this exercise has shown me that I need to recalibrate the analog input levels on the EQ.