For all those that are interested - just found this post which discusses a nice way to deal with this situation, which is what I'm now going to do. The developer automatically sets up a set of SamplerState objects in their engine and set them in the shaders by default. The shaders have a common include containing the register references for all of these so that all shaders have access to set of samplers etc automatically.

[Edit:] Though I'd give a quick update - this method works fantastically - all my shaders now have immediate access to any samplers they might need and its simplified my some parts of my engine code a lot! Works perfectly.

For all those that are interested - just found this post which discusses a nice way to deal with this situation, which is what I'm now going to do. The developer automatically sets up a set of SamplerState objects in their engine and set them in the shaders by default. The shaders have a common include containing the register references for all of these so that all shaders have access to set of samplers etc automatically.