This relates to a cards DirectX compliance. DirectX can be divided into two specifications, the Pixel Shader Model, and the Vertex Shader Model. Each model has different hardware requirements, and when you take both into account you can determine the overall DirectX version.
Think of this number as a more specific description of the DirectX version. Specifically, what geometry manipulation capabilities it has.
Does It Matter
Definitely. This number may directly affect the features that will be available to you in certain games.
Here's a brief description of the different versions:
VS2.0 - Came with the original DirectX 9.0 specification. First implemented in the Radeon 9700 Pro.
VS2.0a - Usually refers to the extended PS2.0 version supported by nVidia's GeForce FX line. Essentially a quarter of the way to full blown VS3.0. It supported far more instructions and features than the PS2.0 specification required.
VS3.0 - Most notably added geometry instancing and dynamic flow control. Also removed the ceiling on most instruction limits entirely and raised other limits significantly. This model is supported by all GeForce 6 Series and higher and all Radeon X1000 series and higher.For more details, check out the wikipedia article.