The schema issues aren't solved by moving to sqlite, or the proposed solution is doable with XML too. I can see the same thing with the attributes (some described it as a shadow schema) happening in an attributes table just as easily. And in my experience relational schemas are a lot harder to modify than a document schema like XML.

EDIT: also you don't need to have just one password vault and I'd say you probably shouldn't, separate entries also assist with separation of concerns. This last adds a little overhead but is a reasonable workaround.

However on the whole I like sqlite for app persistence. It can, however, leak data (forensically) if not managed properly.