Not really, but the most vector/matrix operations make people more busy than remembering and understanding syntax and semantics of language, even though they met the former at school already while are new to later.
Also take note that shaders are not limited with their usefulness to 3D graphics, it's possible to operate with sprites as well. For example it's possible to shift colors on bluesuit and make it redsuit without touching sprites or breaking non-cloth parts (eg. extract blue dominant pixels and make them red).
By the way, from SVN log it's apparent Fonline is going to have windows specific libs replaced by portable ones, and D3D is going to be replaced by OpenGL. This also means there will be GLSL rather than HLSL.
For 3D developers it shouldn't really make much if any difference though.