You can get hints or instructions for crafting from recipe books, but I don't think you can craft with the books themselves.
Generally not. Some keys can be used more than once, though, and some quest items have more than one use.
There is no in-game need to collect the inert star stones (don't know if you can do something with them later... probably not). They are star stones, though. Surely you can spare a few inventory slots of a vase in the End of Time for them? You can't be a hoarder if you don't even collect plot significant items like that.
