How do Dark Side and Light Side points work with regard to your faction

Three shards can be combined using an Assembler to form a Matrix Cube; the cubes are then used in your character's Relics slots. There found on all the planets and only in datacrons.

As far as the number, there are 67 datacrons. However, there are a limited number of shards to be found (3 red, 3 yellow, 3 blue, 2 green--98% sure, again).

Here's a video walkthrough with more details on how to use them:

This is the most comprehensive guide I could find on the locations of the datacrons (including those with shards):

http://www.republictrooper.com/datacron-locations/

They don't have a rating, and they're always shown as neutral. I'm pretty sure their rating scales only show up because it is a part of the character sheet that they don't have something else to display there, although they could be adding it to later versions of the game as well. There was some original talk of the kind of crew missions you sent them on affecting the rating but that obviously hasn't/won't be implemented. (Diplomacy missions only affect your own rating.)

Note however that your companions are limited by your alignment. They can't use items that don't match your character's alignment.