My read is that their APIs weren't ready in time, so "make a web app" was a stop-gap they tossed out to developers while they were preparing UIKit for its 1.0 release.
In another email it seems like before the device was released the need for a native SDK was considered only as a stopgap until HSDPA was fast enough to make web apps good enough (the original iPhone was EDGE only) https://www.techemails.com/p/scott-forstall-emails-steve-job...
"You don’t want your phone to be an open platform. Cingular doesn’t want to see their West Coast network go down because some application messed up." -Steve Jobs 2007