Nope, iTunes is AAC, Apple's equivalent of MP3, compressed thus.
I only have about 3800 tracks in there yet. Another 80 GB is waiting to be converted to Alac and then tagged in iTunes here on my drive. Then about 500 classical and 500 jazz CDs still need to be ripped.
Since you don't have that much music yet, now is the time to set the metadata and classify them all in the way you want your music to be organised. The each time you add new music or rip a CD it's a breeze to make it fir into your system.
Believe me, it isn't much fun to do that with thousands of tracks all at once.
If it's for playing through iTunes that won't change a thing. You need to shut down iTunes, change the setting like Paradoxper said and the relaunch iTunes each time you use a file with a different sample rate. Not a bug, Apple is very well aware of it but they're pretty stubborn buggers. I guess they don't feel the need to change the sample rate since they want you to buy all your music from the iTunes store.
If you don't do it that way, A/M Setup will show the correct sample rate but when you have an external Dac you can see on the Dac that iTunes is still using the previous sample rate.
Or simply install an app like BitPerfect that does that all automatically for you without shutting down iTunes.