Both Command keys as well as zero digit not functioning on MacBook keyboard
Your keyboard is failing and should be replaced.

The keyboard is made up of "layers" with one of them being a flexible plastic "circuit board" with conductive traces.  The photo below shows a typical example of this (Disassembled keyboards from MacBooks aren't common so I used a PC keyboard - the technology is the same).  

Update:  I wrote a canonical Q/A on this topic that shows much better breakdown of the keyboard assembly and goes in depth as to what the issues could be.



The keyboard recognizes a key press when a particular circuit (or circuits for multiple key presses) is/are closed.  It's a physical connection being made.

If anything gets between the contacts or if the contacts become worn, the keyboard will begin to malfunction as yours is doing now.  

This will only get worse.  Keyboards don't fix themselves and software fixes only go so far.  Your best bet is to replace the keyboard - and there's good news and bad news...

The good news:  A replacement MBA keyboard is relatively cheap; less than $20.



The bad news:  Replacing the keyboard will require you (or a tech) to completely disassemble your MBA.  This involves literally taking every single component out of your MBA.  It's not a hard process, but rather a long and detailed process.  Ifixit.com has an excellent step-by-step.

If you feel comfortable around electronics and you have done this type of thing before, I recommend that you give it a go at replacing it yourself.  

If this is not something you are comfortable with, I suggest hiring a tech.