Why some vias have solder mask and others do not?
It's an option in most PCB design software, both as a default and on a per-via basis.

The advantage of leaving the vias uncovered is you can probe them with test probes without having to scrape away the solder-mask first. The advantage of covering them is reduced risk of shorts or solder-stealing.

Personally I tend to start with them uncovered, but then cover the ones close to components. 

I wonder if in your case the designer has made them covered by default on the power/ground nets, but uncovered by default on signal nets. That could make some sense as power/ground vias are less likely to need to be probed and are more likely to be in tight locations.