Yes, if run at 64x or higher time compression the crew will not loose (or gain) any fatigue.
In standard SH3 the crew will loose fatigue in all compartmens except for the quarters, where they will also recover from fatigue at 32x or lower time compression.
There are mods out there that will reduce fatigue or remove it altogether, and there are mods that makes it even harder to keep your crew working, like it was in real life..
But an automatic crew rotation would be nice, but unfortunately this is not modelled. Well at least it gives you something to do on those long cruises with no action...