Well, speaking to the larger point of fleet control rather than pirates, speaking as a relative newbie I can say that I think the whole ship/fleet UI leaves a great deal to be desired.
Part of the problem is the UI's rather distressing tendency in various places to refer to ships by their (colorful but useless) name, instead of by ship type. E.g. in the construction yard menu, you either have to recognize the ship profile or click on Show Construction Summary to know what's being built.
Similarly, when you select a fleet you are presented with an array of ship icons, but nowhere (at least I haven't found it) is there a list that says this fleet consists of so many escorts, destroyers, etc. And there is apparently no split fleet dialog either. Which means that it is so much trouble to rearrange fleets that I simply leave them the way they are and construct new ones if necessary.
This may be a bit tangential to the OP's point, but it's been bothering me, so I horned in.