I have actually been calling for a blind pick for awhile. This is a great idea that is already commonplace across most competitive communities. Currently, it is still just as easy to be counterpicked. All that happens is that the teams will take turns changing their ships in the lobby until the timer runs out, and then it's whoever scrambled to get their crew ready in time gets to counterpick the other one.
However, one genre of game that doesn't do blind pick is the MOBA genre. With many picks to take (usually 5 per team), a MOBA system can evolve on the blind pick to create a whole draft mode. Lueosi actually said "tactical drafting" in his original post, and blind picking isn't actually that much of a tactical draft. While it does make the picking system more fair and less clunky, it does have the downside of possibly allowing you to be counterpicked without having an opportunity to do anything about it. Instead, a typical draft system could look as follows:
We have ships 1-1 and 1-2 on the same team, and ships 2-1 and 2-2 on the same team.
Ship 1-1 picks chassis (main ship, like junker, goldfish, etc)
Ships 2-1 and 2-2 pick chassis
Ship 1-2 picks chassis
Ship 2-1 picks guns
Ships 1-1 and 1-2 pick guns
Ship 2-2 picks guns
This gives a solid structure to the picking system, allows you to respond to opponent counterpicks, and generally leads to more balance between the ship loadouts. For example, if ships 1-1 and 1-2 counterpick ship 2-1 after their guns are set, ship 2-2 has a chance to counterpick ships 1-1 and 1-2. Regardless, I think blind pick is a step in the right direction and much better than what we currently have, though I believe a draft could work better.