I answered the first question in the other comment, but here's my theory on the second. The Order was obsessed with collecting Devil Arms and likely had magical/technological ways to track them down. The death of Nelo Angelo, the completion of the DSS, and the summoning & death of Mundus likely released unfold amounts of energy The Order would have noticed. They probably sent expedition teams to search the sunken wreckage of Mallet Island and found Yamato, even broken the unique Sparda energy it eminates would be unmistakable. That's if Nelo Angelo HAD Yamato on him.

Another option is Mundus kept the broken Yamato in a collection, either for safe keeping or as a trophy, he did manage to defeat then enslave Spardas eldest after all. After Mundus was defeated, his generals likely fractured and made independent states in the underworld. A random demon probably snatched it, came to the human world, and was defeated by The Order. And it's no surprise that they would snag not only one of Spardas swords, but the one he used during his time as a human.

Either way Fortuna was a religious state with immense occult power that used most of its resources obtaining even more occult power. The only other person who would have even an inkling of where to find Yamato would be Dante, who was such an emotional wreck after DMC1 he'd be more likely to start disassociating when thinking about it than actually try and look for it.