There are multiple ways of looking at this, high quality 12V LEDs are hard to find and can be quite expensive... however some people are very satisfied with the 12V LEDs that are available. Transformers also waste energy but the efficiency can vary greatly. As long as you are on the grid, I would use higher voltage LEDs since they're cheaper and you'll use less energy. But if you do go off grid, you can run the 12V right off your batteries. This can be a nice advantage, especially if you use a 12V battery bank; however, most quality off grid systems use 48V as a first preference or 24V as a second choice, so you would most likely need a DC to DC converter (or power supply) in order to run 12V anyways.
I guess that is really is a matter of preference but I would go for the simplicity of easier to find, high quality, higher voltage LEDs, with no transformers wasting your energy unless it is important to be able to use it straight off a battery