1) After the kill the loot cargo boxes drop into space. What's the secret to picking them up? It seems I need to hit them just right under my ship. Any suggestions?

2) Do the different color boxes represent anything? Is one worth more than another? Are some resources and others ship gear?

1) fly through 'em
2) purple = ship equipments, blue = commodities, green = ore, brown = scrap metal, yellow = bot cores, white = CtC purified Xith

If the loot is more than your ship's cargo capacity you won't be able to pick it up. Small fighers with 2-8 cu won't take 200 cu load of an XC.

in 3rd person view it kinda looks like you need to ram the boxes just below but in 1st person view just point your crosshairs right at it and you won't miss

Thanks guys. Excellent responses :)