There's no official "way" or set standard to do this, and it's mainly up to how the programmer & artist would like to do it. But since you don't have a system, perhaps you should just use bones and put a joint there? Again, the system is set by the engine you're using/programmers.

There are a couple things you can do.
First, you can use a bounding box via the game engine as a collision mesh (or for other things).
You can also create a seperate collision mesh via a modelling program.

Generally 'fire effects' and the like (like the ones in Oblivion), as far as I reckon, use shaders and effects along the actual mesh (on the surface). There are also particle effects that can use a mesh/geometry as an emitter.

So for things like fire effects and particles, most won't be done via 3ds/maya. For collision meshes, it will.

EDIT: Joints and bones are used for animation... adding them would generally not be part of the particle/effects pipeline, unless you are using it for some interesting things (Such as applying a certain effect at certain intensities depending on bone weight?). So for your example I don't think its part of the equation.

Ah. What you'd want to do, then, is have the hilt of the blade (or some recognizable constant area) lay at 0,0,0. That way, you can reuse the same weapon animations, and regardless of hilt or blade length they'll all work.
For the effects, probably having the effect follow world space along the mesh (from the lowest point to the highest point in space) would be best.
Also dividing the mesh into chunks could work (ie, seperating the blade, so the hilt isn't effected).