The Register received word directly from Apple that web apps are in fact running slower on iOS 4.3 because they're not optimized for the new Nitro JavaScript engine.

"The embedded web viewer does not take advantage of Safari's web performance optimizations." Apple spokeswoman Trudy Muller tells The Register. It would seem that these optimizations include the Nitro JavaScript engine as well as certain Safari caches and the browser's "asynchronous" rendering mode.

Apple is offering no comment on whether or not they'll update this in the future. [The Register]