Since you were shooting at f/16 and around 1/30 or 1/60 s. (ISO 100) the scene that day was around 13 EV (see an Exposition Value table here https://en.wikipedia.org/wiki/Exposure_value#EV_as_an_indicator_of_camera_settings).

Using an ND4 filter would take you to a ~9 EV situation, so in terms of autofocus you would not have any problems, since EOS 6D is capable of focusing even at -3EV situations (as Canon states in their webpage) as long as you use the central AF, which is the most precise.

ND filters would enable you to stop down [edit:] widen the aperture, so you can get a more blurred background. However, this blur is what we know as bokeh and it is different from the motion blur you mention at the beginning of your question.

Obviously, a wider aperture will make the background look more blurred but if you are looking for that motion blur you mention, you should practice a technique called 'panning'. And when 'panning', the piece of equipment that will help you the most is probably a lens with image stabilization (Sigma's HSM, Tamron's VC, Canon's IS...), though it is not indispensable at all.

'Panning' (https://en.wikipedia.org/wiki/Panning_(camera)) is a difficult to master, but very funny technique consisting of shooting with slow speeds (1/10, 1/15, 1/30, 1/50 s., for example) and following a fast-moving subject as you expose the photo, so it will look sharp (or sharp enough at least) while the rest of the scene is motion-blurred in the direction of the movement. You will need SERVO autofocus, slow shutter speeds (go for S or M modes) and a nice, stable position while shooting.