Yes, this will, or at least should, make a difference.
The reason is that Windows Store apps are actually wrapped in a sandbox environment. This means that your actual Windows environment, including your registry, will not be littered with rubbish.
It also means that, not only will iTunes be updated for you automatically by the Store, but if (when!) you decide to uninstall it, it will be totally gone. Unlike the standard installation that leaves behind all sorts of rubbish that slows down your PC.
Here are some articles that describe the Windows Store Sandbox and its implications:
- Desktop vs. Windows Store Apps: Which Should You Download?
- Building Secure Windows Store Apps
- S is for Sandbox: The logic behind Microsoft’s new lockdown Windows gambit • The Register
- Windows Store Apps live in the Sandbox - SogetiLabs
And one more link that is relavent to the Windows Store version of iTunes as this is very likely how it has been built: Desktop Bridge – The bridge between desktop apps and the Universal Windows Platform – App Consult Team
Unfortunately, the expected raft of announcements on the various tech news sites, as so often, miss the whole point of why this is an important release. Most make no mention of the protections, performance and update benefits or if they do, they don’t explain why they are important: