It kindof depends on the scenario. For a production trunking system, site-trunking is something that should almost never happen. It means that the site has been cut off from the rest of the system, and so is operating (limping along) independently. If it's part of an extensive system, most the subscribers may move to a different (nearby) site when this happens, so having site-trunking enabled may actually not be what you want.
One case where I have intentionally enabled site-trunking is the new CA state-wide system (CRIS) that's currently under construction. It has sites which are currently in site-trunking mode some of the time, because the system is not live yet. I plan to turn disable site-trunking in my profile when it does go live.
Generally I would suggest leaving it disabled, and not worrying about it, unless you have a specific reason to enable it.