A conjurative focus can be used to see if something is a reagent. This seems to nullify the point of the conjurative sand. Am I missing something?

I don't think the conjurative focus will actually check to see if what you're trying to use as a reagent is actually a reagent.

I used the summoning focus on an item and it gave me the message "XXX has been chosen as your reagent" or something like that. I used the sand on it afterwards and sure enough, it glowed. Was this just a coincidence that the item I targeted with the focus was a reagent? Would it just as soon say "Longsword has been chosen as your reagent" if I targeted a longsword and summoned the normal summon for that level?

It should behave like that, yes.

I suggest trying it out in-game, to get the quickest possible answer!