You need to look a bit closer to see the difference.
APU uses cheaper realtek NIC and soekris uses Intel's.
Soekris gives Intel QuickAssist to help encryption (VPN etc.). And soekris is showing up a new model later this year: http://soekris.com/products/net6801.html
But PC-engines boards are nice for their price. I'm considering to get one at home. That or spend a bit more on soekris box/