Unless the liquid system in question is located inside a giant bathtub that's enclosed on all sides and has some sort of force keeping the liquid in place, there won't be any pressure acting on a ship flying through it: the liquid will just move out of the way.
To be more specific, there will be pressure acting on a moving ship at its nose, where it is colliding with the liquid like an icebreaker. But if we design ships that can withstand atmospheric pressure when they lift off from planets, I don't think this would be a problem.
EDIT: I would imagine that a system full of liquid would look more like a bunch of individual droplets floating around in space. But that would be pretty lame, hehe