See, the problem was that the logs you posted very definitely had nothing to do with TBP.
Anyway, let's see about the list of questions.
1. Yes, shaders will always be used if they are in a mod's "data/effects" directory.
2. How are they used? Well, a shader is a program that is run on your GPU to create images. Each shader is made up of a vertex and a fragment shader program, which is compiled by the display driver and uploaded to the GPU. These programs are used to handle parts of the rendering pipeline that used to be fixed-function; Vertex shaders handle vertex transformations and setup, while fragment shaders generate the actual colour values for pixels.
3. The engine will compile all shaders used during startup. The only exception are the post-processing shaders, which are recompiled on the fly if the post-processing setup changes due to sexps.
4. You generally do not know which shader the engine is using at any given time. This information is not printed to the log, because it is generally useless. However, you can generally infer which shader is used if you know the combination of texture a given object is using. In the log, you will find compilation messages following this format:
Compiling shader: <vertex shader filename> (<decomposed filename>), <fragment shader filename> (<decomposed filename>)
In the case of main shaders (which are used for all model-rendering related duties), the decomposed filename indicates which shader flags are active, and this information can be used to figure out which shader is used for a given model. Here's a list of possible flags:
l : Shader handles lighting
f : Shader handles fogging
n : Shader handles normal maps
e : Shader handles environment maps
a : Shader uses animated effects
b : Shader uses diffuse maps
g : Shader uses glow maps
s : Shader uses shine maps
One note about the shaders floating around at the moment. They are ALL written for 3.6.13/3.6.14 builds, and WILL NOT WORK CORRECTLY on 3.6.12. They do incorporate a few advances (such as anisotropic lighting and per-fragment lighting) which rely on information provided by the engine to the shader only available in 3.6.13 and later builds.