I don't think they're souls. In the movie Hercules, the souls were in a green river, not floating blue orbs. So I guess they're not souls. Maybe they're yokai or something...
That is what I was saying earlier. However, I don't think all souls were in that river (if you mean the river where Megara was thrown into for Herc to rescue). That river I think is called the River Styx I think and it is a river that ages people rapidly until they die. However, I don't think souls were in that river. I read somewhere that they had to do with gods being in there.