Yes, with the free version, we always do update checks, we just give the option to install them.
In a typical year, we need to do 2-3 releases just to keep compatibility with Windows and driver updates. Some of these issues are pretty serious, and they are mostly out of our control, but we do our best to keep things working well.
Think of it this way: with many millions of users, we cannot handle telling people by hand to go update the software to the latest version - our email just does not scale like that! So if we did not do updates like this, we would have millions of broken f.lux installs and no way to fix them.
We do have a commercial version if you would prefer to receive emails about updates instead - this version never talks to the network automatically:
https://justgetflux.com/corp/