Amduat Ink and Abydos Commom are trials rewards. You get them by going flawless on a character and then continuing to play trials on that character. They are extremely rare drops so that's why you don't see them often. The crucible ships, as far as I know, are only obtainable from the weekly bounty. I've seen a few people with them and they all said that's how they got it. As for everything else, I assume that they are either glitched or just not obtainable yet for some reason.