For science codes, where Fortran is still used, the most expensive pieces (think DGEMM Kernel) are largely written in architecture dependent ASM anyways so programming language doesn't have that much of an effect on the most time critical pieces of large HPC programs.

If a specific function is important enough it will be hand optimized in a way that the language doesn't really matter. Sometimes that means calling MKL, or using Cuda, or writing your own assembly.