Here are the answers to your questions:
1- VT-x extensions must be enabled when working on a virtual environment only. The Operating System (host machine using ESXi 5.5 as an example) will use these extensions to install the Operating System successfully and ensure the functionality of the virtual machines. If you do not have a virtual environment you will be calling BIOS features which the Operating System will not take advantage of and that will increase the CPU usage for no reason.
- The CPU will not run slower neither affect performance or security, is just the simple fact that you are enabling extensions that a regular Operating System will not use at all.
Forgive me for being picky, but you state in the first paragraph that enabling VT-x without using virtualization will "increase CPU usage for no reason", and then you say in the second paragraph that it will have no impact on performance. If the CPU is busier, then surely performance will be impacted on a heavily-loaded system as those cycles are not available for use by other processes.
Again, why would BIOS developers include an on/off switch for this feature is turning it on has exactly NO ill effects of any kind?