As noticed by CNET, a thread on Hacker News shares that iOS 5 does in fact provide home screen web apps with access to the Nitro capabilities, making them comparable to their directly-loaded counterparts.
Q: Did they fix the bug from 4.3 where home screen web apps don't use Nitro?
A: This is probably breaking my NDA to say this, but yes, they did. Web.app now has the "dynamic-codesigning" entitlement, which enables Nitro.
The thread goes on to reveal that the Nitro implementation does not extend to web pages loaded within other apps that take advantage of UIWebView to provide browser functionality without redirecting users out of the app and into Safari directly. That omission is reportedly due to restrictions that prevent the Nitro entitlement from being extended to all apps for security reasons.