I am not looking forward to managing fighter fleets because of that. The Ship Combat tab is more of the same.
For fighters - select the fleet that has them and go to the fleets ship list (not on the naval OOB, the tab of sections that have the movement commands etc.). On that shiplist you actually can shift-click multiple fighters, when they are all highlighted, click either "create sub-fleet" or just "detach" and you have a fleet/sub-fleet containing nothing but your fighters. Now you can effectively handle 100s of fighters without having to drag and drop them one-by-one.
With sub-fleets, combined with the "dock at assigned mothership and join as sub-fleet" this allows you to also name you fighter wings and have that name persevere through docking/undocking.
The ship combat tab absolutely needs shift-clicking in order to select multiple weapons and drag them at once. Especially true for missile ships that have 10s of missile tubes.