Both of the points you bring up are unrelated to the format in which files are stored. Sure, they would be requirements for the format that gets sent to a primitive DAC. But the answer to your problem is basically contained in your post: before the signal is sent to your theoretical DAC component, the signal's rate could be digitally upsampled by a factor of 2 (to avoid artifacts), and dither could be applied to eliminate any jitter problems (with the unnoticeable side-effect of raising the noise floor to -66dB, in the case of 16 bit depth).
Anyways, as dfox mentionned, most sound cards nowadays use sigma-delta DACs, which do not need upsampling as they do not involve a filter in the way you described.
Anyways, as dfox mentionned, most sound cards nowadays use sigma-delta DACs, which do not need upsampling as they do not involve a filter in the way you described.