Kontakt will make more efficient use of resources with fewer instances, so overall efficiency will be better with a single instance in multi-timbral mode.
However, the improvement is marginal. By far the most significant resource is memory, and that's mostly determined by the libraries themselves and won't increase or decrease based on the number of Kontakt instances.
Furthermore, when you use a single instance, you lose the ability to freeze each instrument independently. So if resource management is a big deal, such as somebody trying to squeeze giant libraries into limited RAM, then you may be better off with separate instances that you can freeze when you're done with them. Or at least purge the sample sets to reduce their memory footprint.
If, however, CPU is your bottleneck rather than RAM, then a single instance will definitely be more CPU-friendly. Each individual instance will use the first core, whereas with multiple instruments Kontakt is smart enough to at least attempt to use one of the other cores (assuming multi-core has been enabled).
My own method is a compromise between single and multiple instances. I combine instruments that are likely to be frozen as a group, such as a string section made up of 3 or 4 libraries, or a percussion group. But the big instruments that I'll be editing throughout the project (e.g. large guitar libraries) get their own instance.