Yes, one can use 2D interfaces inside 3D worlds but any 3D system short of the matrix will have a noticeable quality degradation (e.g. visual fidelity, haptic feedback, fatigue, etc) compared to directly using a 2D interface in real life. A few edge cases might become feasible much sooner, e.g. using VR to emulate large screens but that's hardly 'Virtual Reality'. Until we come up with meaningful ways to represent more kinds of information in 3D and/or create a matrix-style experience, VR will most likely be limited to applications that are inherently 3D.
This obviously includes entertainment (VR games, 'movies', 3D art) and CAD/CAM/3D modelling which are already very much 3D in nature and internal representation, even if they are currently usually projected onto 2D screens. Outside of that, the main 'educational' usage currently consists of building 3D environments (labs, buildings, factories, complex machinery) that emulate real-life environments in order to familiarize trainees with the workflows in those places. This can be surprisingly effective, especially considering how much cheaper VR mockups are compared to e.g. NASA's real-life 1:1 ISS training replica.
These applications are worthwhile in their own right and they will probably be able to sustain a decent market for VR hardware and development. However, I'm personally much more interested in seeing what kind of concepts that aren't already inherently 3D can be enhanced or revolutionized by adding another dimension.