Relative forms are a means of namespace abbreviation. Query syntax is simply a convenient mechanism for parameterized access to a resource, which exists only for the sake of common client implementations.
Fragment identifiers are a mechanism for identifying a subset of the result of a retrieval.
Whether or not all of these are only part of the application of hypertext depends on your definition of hypertext. Hypertext can be usefully defined either in terms of the UI or the architecture. Keep in mind that my protocol library was original written to support maintenance applications, not dynamic display. The architectural definition of hypertext is simply that information can be organized by relationships between information, and further that resources can be organized by the relationships between representations of those resources. This definition does cover all of the controversial syntax forms, but then it also covers all possible uses of URNs as well, including semantically rich name comparison.