Does Google have five million of these phones sitting in a warehouse? I doubt it, they probably manufactured based on historical Nexus sales figures, and I'd guess that the fact that this is sold out just means it is selling better than previous Nexus phones.
EDIT: I can't find a good source but my best estimate for the sales of the Galaxy Nexus (i.e. Nexus 3) is 100,000 per month based on sales of $250M over 6 months at $400 ea. [1]
[1] http://www.theverge.com/2012/8/20/3256590/samsung-galaxy-nex...
Let's say they had a quarter million units for sale for their first run (given their Nex7 sales, totally reasonable). That means they're selling ~80 phones a second.
Now did Apple sell more? Sure. Does that mean these numbers are bad, even in a relative sense given the obscurity of the Nexus brand, the troubles during launch and the location of sale?
No. Supply or Demand, this is good for Nexus.