Are there any disadvantages to enabling Intel hardware virtualization in BIOS settings?

Every feature in the platform has the possibility of providing a means for malware to gain control. I’m not aware that VMX is susceptible, but it seems like a reasonable precaution to leave disabled features that you don’t need.

If you need it occasionally, it is perfectly reasonable to leave it enabled all the time. There is no harm to the hardware nor any additional power usage or performance impact in having it enabled in the BIOS but not being used. I think this would be safer than changing it in the BIOS every time it is needed.

However some operating systems may automatically make use of it if is available. They would do this specifically to reduce the risk of malware and contain the impact of bugs in the system. In this case, there may be some additional power usage and performance impact, to obtain the benefit.

There was an attack in around 2006 called blue pill, that used virtualization to create the so called virtualized rootkit, a rootkit that should be undetectable.By virtualizating the target os while hiding itself The attack spanwed countermeasure by bios manufacturers, that disabled the virtualization extension by default.

There was no virtualized rootkit found in the wild, and the attack proved to be detectble ( timing attacks, and other holes in the virtualization). The attack lost of its relevance and today the BIOS settings represent the panic that surrendered blue pill. If an attacker would gain ring zero acssses that would allow him to create a virtualized rootkit, most of the chance he wouldn't create it, and if he would it would not be much scarier then a regular kennel rootkit.