Well, it's possible to create an empty fleet if you have 2 ships, detach one, then drag&drop it back to the previous fleet and the 2nd fleet (now empty) remains. But I did not find the possibility to create a fleet without ships from the beginning.
Unrelated, is this still a thing that commanders will be dismissed after 5 years if they don't have a command? I have a bunch of naval officers I would prefer not to lose, and I can certainly roleplay they are staff officers, commanding a shuttle
And also ... why not check ECCM for STO, it does not change the cost?
They should always have the 'avoid combat' check on, right?