In practise, the YM2612 DAC gets updated with only 27 KHz (half of the chip's output rate), but the odd timing resolution of 44.1 KHz indeed introduces jitter. This is unfortunately a historic limitation of the file format.
The 44 KHz rate is fine enough for normal listening though, because most games don't go over 24 KHz for PCM samples, so the jitter isn't very noticeable. The very common GEMS sound driver even does only 10.6 KHz. Many games also suffer from heavy jittering introduced by the sound driver pausing PCM playback for a few milliseconds once every frame, which further hides artifacts of the VGM format.
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