In-Kontakt multicore allows parallel processing of voices. Disabling this means that a single instance of Kontakt would use only one core (at any given moment in time), and multiple instances of Kontakt would distribute over processors based on whatever your DAW's behavior is.
In other words, DAW multithreading and Kontakt multithreading are independent and both can theoretically be enabled as they parallelize different things. I set my Kontakt core count to 4 to allow for some parallelism within a given instance, and my DAW thread count to 32. (I have 32 logical processors.) In practice, how cleanly these interplay is also influenced by DAW behavior.