Please upgrade your Yún - latest is 1.3

Using hypervisor compare with bear metal will lost % performance, and different type hypervisor will be vary.
Worst case you got hit by 80%

VMware Workstation and VirtualBox is type 2 hypervisor will be suffer more than type 1 hypervisor.

OpenVZ might be best fit: it does not have the overhead of a true hypervisor, it is very fast and efficient. The disadvantage with this approach is the single kernel. All guests must function with the same kernel version that the host uses. My personal experience only lost 5~10%.