The seasonal flu also mutates. The annual vaccine still helps prevent it or lessen severity.
They adjust the vaccine annually to account for some of the mutation.
I think it will depend a lot on what the mutations do. A very recent report here in the US showed that the mutations had not increased it's danger or severity.
Edit: I only learned this yesterday. We STILL vaccinate against the strain of the flu that caused the 1918 Spanish flu. I'm sure it has weakened, but it is still a part of the annual flu. (Type A)