Obviously a host can modify a virtual machine in any way and has full control over it, but in practice perhaps most viruses wouldn't have the complexity to search for virtual machines and modify them. Although simple keyloggers I assume would still remain a threat.
Anything which is different from the attackers expectation increases the efforts needed by the attacker and thus slows down attacks. And if the additional costs are high enough it might also prevent attacks since they are no longer worth the efforts. Running a VM inside a compromised host is no different to this.
But, if others are using the same kind of setup for added protection it will be no longer different from the attackers expectation: Attackers will catch up and consider this kind of setup too and invest time to efficiently handle this setup, since it would be worth the efforts. Thus, it might help in the short run but it will not help in the long run if others are doing this too.