WELCOME ABOARD!
Yes indeed, SH3 Commander lets you set the crew to 'No Fatigue', along with a wealth of other cool stuff. The fatigue problem was complained about almost as soon as the game was released, and the devs fixed it, but not in SH3. SH4 has actual watch bills and automatic shift rotations, so get ready for GWX4 in the near (or perhaps not so near) future.