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

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.