First question:
If you have installed a fragment shader, must you also supply a vertex shader or will you still be able to use openGL's fixed functionality for that portion of the pipeline?
Second question:
If you are using matrix palette's and vertex blending, but then switch to a vertex shader, must you calculate the final vertex yourself from the weights and palette or will open gl still do that for you?

if you are mixing shaders and ffp remember using

gl_Position = ftransform();

instead of

gl_Position = gl_ModelViewProjectionMatrix * gl_Vertex;

to gain transform invariance. otherwise you will get artefacts...

There actually shouldn't be any difference on most shader capable GPUs since they no longer physically implement the fixed function pipeline.