Users have been conditioned to judge startup time by the number of times an icon bounces in the dock. Chrome is only perceived as fast because the feedback is different from the other applications. It's all relative. Once enough developers start using this trick that perception is ruined and developers will have to resort to splash screens and progress bars again.
But the point is that the app is already loaded. It's just shifting the burden of loading from dock click to startup. The users probably won't notice that their system takes longer to start because it already takes so long compared to the loading of one application. (At least for most systems. I try to keep it as short as possible.)
If lots of developers do this the negative effects will be longer desktop loading times, the time from login to usable desktop, and more idle memory usage. With memory so cheap, I wouldn't be surprised if this becomes more common, though personally I think it isn't polite to the user.
Actually, no. The program still starts up when you click on it except it doesn't register itself as a foreground application until after it is loaded. The time to start the application is exactly the same, bootup time is unaffected, but the icon just doesn't bounce.