That could be true for general consumers, who could be scared into disabling Java altogether in their browsers(so that some part of the population wouldn't be reached by the app). On the other hand, if you're making B2B/scientific app for a specific niche, your target audience should be interested enough in what you have to offer so that, even if they disabled Java, they'll turn it back to check out your app. In other words, people will gladly suffer minor inconvenience for an app that adds value, while would be probably put off if the app is another social network/messaging app/game etc., where the perceived value is vague at best.
Yeah, you're probably right...I hope...and Java still seems to the only game in town for unified web + desktop functionality.I just don't see another choice.
My understanding is that web apps have some limitations that can be a show-stopper for scientific apps - for example, there's no way to gain an arbitrary access to file system (something that is easily doable with a signed applet), which can make bulk processing/import etc. impossible. That's the reason I recommended applets in the startup I work for.
