Well, the Uzumaki weren't really massacred like the Uchihas. It was mentioned a couple of times that their country, which is, Uzushiogakure was destroyed during the previous shinobi wars and that the survivors fled to other countries. So technically, there are still Uzumakis all over the ninja world.
I think Uzushiogakure was attacked by many other countries during the war (First, Second, and Third- possibly). It's not impossible since they were also allied with Konoha back then, so they'd naturally be targets for enemy countries. Not to mention that ninja world back then was pretty much unstable.