Hi,
After doing another test, I can now confirm that the logistic skill of a captain don't alter the loading or unloading of installations, minerals and troops.
Basically, from an answer from Steve, logistic seems to be only used by planetary governors (and perhaps sectors governors, for planets).
That's quite meager... Except for RPG purpose, adding a captain with good logistic to a troop transport or freighter is thus useless. Is something changeable and doable in the future about that, please?