The cynics view would be because as the web app approach becomes less distinguishable from native apps speed, those web applications end up running as well on equivalent speed hardware such as Android and other platforms as they would on iOS, ceding some of iOS advantage in the richness and diversity of its applications.

However it should be noted most of the popular applications in the iOS app store are in fact games

The real reason is likely to be more to do with security around the js runtime, especially when UIWebView is placed in "wrapped" applications

Or just a bug due to the setup process of UIWebView or "offline" webapps not enabling Nitro where Safari's usage of webkit does.

Does anybody have insights into general performance implications of using UIWebViews vs Mobile Safari?

There are several, but in particular, JavaScript seems to run 2X slower in UIWebViews vs Safari. on iOS 4.3

From what I've been able to find, UIWebViews run as they traditionally have on 4.2, the JS just runs 2x faster exclusively in Mobile Safari, so no performance hit, just no gain either.