According to information from appleinsider, ios5 beta fixes that problem and now Nitro JavaScript engine enabled on Web.app.
I've iOS 5 installed on my iphone4 and updated SunSpider JavaScript testing framework 0.9.1 (to be able to start as fullscreen web application under ios). And I've started subspider several times in fullscreen webapp mode and in Safari mobile. So, see my results below (images are clickable):
May be something was fixed (apple insider provides 4 vs 10 seconds difference), but I can't say that performance is equals in both cases (3756.5ms vs 5243.8ms for those who can't see images).
UPD
Small interesting note about UIWebView, it is impossible to use Nitro-enabled JavaScript engine in native applications (I mean applications designed in Xcode and posted to AppStore) because Nitro JIT requires to be able to use dynamic code signing.
UPD
Look at iOS 5 Top 10 Browser Performance Changes on blaze.io, Seems Apple enabled Nitro for Fullscreen WebApps in iOS5 (nice statistics in article).