Apple's philosophy is that a well-designed, tightly integrated product will always be superior to one designed with loosely-coupled interchangeable components. That's the reason they didn't give up on Macintosh throughout the '90s, when everyone else was going to Windows.
By this reasoning, Apple doesn't see web apps as a threat to native apps. Because of limitations in web technologies (today), they are less capable than native apps. Apple is so confident of this that they see no problem with improving the capability of web apps: adding touch event handling, location services, offline access. If they wanted to discourage web app development, they would not provide these APIs.
Yes, Apple doesn't make any money when somebody installs a web app, but it doesn't cost them anything either. Some businesses would consider every web app sale to be lost revenue on a hypothetical native app, but that reasoning is shaky. Intentionally crippling their product to undermine web apps would only put them in a worse position should a killer web app (that runs better on Android) came along.
To date, Apple has done more to promote native apps, for obvious financial and technical reasons. But they have also supported web apps, and done nothing to inhibit them. I don't think there are any "hardships lurking"; the limitations are out in the open, and reasonable.