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Isn't there that "Quick Dock" button or whatever it's called that lets you skip the waiting and instantly puts your ships into position for the hyperspace jump? As for whether you have too many ships, well I've never captured quite that many so I wouldn't know what to do about that.
I think quick docking is for single player only, not multiplayer. A button at the top left should come up when you hyperspace. And again there's a limit to how many ships there is during single player, but theres a option during the multiplayer options screen so there is no restrictions.