You honestly think that Apple would deliberately hamstring javascript performance on the iPad so that people have to use native apps? I think it's pretty ludicrous to think they'd do that: their sales of the iPad are directly, heavily affected by perceived performance of the device. If it's slow, people won't buy it.
How many extra apps do you think that move would make people buy: 2? 5? So you think they'd cripple performance and lose hundreds of thousands of sales so that they can get people to spend an extra $20 or so at the app store, of which they'll get all of $6? If they wanted your extra $6 that badly they'd just up the price on the device.
I just don't understand this constant assumption that every decision Apple makes is anti-competitive and designed to achieve lockin. Isn't it way more rational to assume that they want to make the device as good as possible because they make money by selling devices, and that their decisions are primarily driven by that motive?