My understanding, first off, is that the OS / hypervisor patch only mitigates Meltdown, not Spectre.
Second, you patch the hypervisor to prevent a VM from reading memory belonging to the kernel of the hypervisor. You patch the guest OS to prevent a process from reading memory belonging to the kernel of the guest OS. My understanding is that they are independent of each other; patching one has no effect on the other.
Emulation vs Virtualization
I'm not a great expert on virtualization technologies, but your question dips into emulation vs virtualization: in emulation the CPU, including all registers, caches, etc. is fully simulated in software and it may use a different instruction set from the underlying hardware. In virtualization, the instructions are passed directly to the hardware, but with extra process scheduling imposed by the hypervisor. In particular, my understanding of x86 virtualization, specifically Intel's VT-x technology, is that it is a "real CPU" in the sense that the guest OS is using real x86 instructions that are more-or-less passed straight through to the underlying hardware.
So yes, the guest OS will be vulnerable to Meltdown and require patching independently of whether the hypervisor has been patched.