After spending 12 years working with thermal analysis teams in the Telecom industry, I can tell you that adding vents (especially on the sides!) makes very little difference.
To increase the cooling effectively, you would need to thermally bond the heatsinks to the case or use some type of forced air cooling.
Adding vents to the sides does little or nothing because hot air flows like molasses.
I think the new version had vents designed on the side as to coincide with the introduction of the M-Stage DAC. Question is though, if the devices were stacked on-top of each other (as pictured), which order would the devices stack?
I figured running the amplifier on top would allow for heat to disperse from the unit faster, though at the same time, it would conduct heat from the DAC below it (even though the DAC outputs considerably less heat). Having the DAC on top instead could mean it conducts all the heat from the amplifier, and the amplifier would have less ventilation. I'm not sure what the best scenario would be.
I suppose alternatively, you could run both devices on their sides, so the heat can escape upwards through the side vents. Doesn't look fancy though.