Although the thermostat was only recently discovered as missing from Apple's product offerings, it was removed earlier this month. Apple was amongst the first retailers to carry the Nest when it debuted in 2011. Not surprisingly, it has already been replaced with the first HomeKit-enabled thermostat, the Ecobee 3 ($249).
It's unclear if Google has plans to add HomeKit support to the Nest, and if it does, whether Apple will return it to its stores.
You can learn more about the Ecobee3 thermostat here.