How do you effectively use a Navigator/Pirate/Assassin combo to kill someone's specialists? Here is the current situation I'm in. I'm losing really badly. I have a bunch of specialists, including the combo stated above. The only outpost I really have control of is a mine. I want to eliminate my opponents queen, which is located at a nearby factory. It has a ridiculously high shield and I can't overcome it's defences. If I sent my Queen Hunter at it, can't my opponent just send his queen away right before I arrive so that I don't have time to reroute my sub? I wouldn't capture the outpost, so all my specialists would be captured. Does a queen hunter need a lot of drillers on board to actually be effective?

Since you have the navigator and pirate (instead of just one of those), you are guaranteed to get Queen unless 1) you are unattentive, 2) he moves into the fog of war, or 3) she hires a pirate to counter your Queen hunter.
If you won't be online at the time of arrival, just navigate to an outpost so that the travel path will be close to the outpost with the Queen, so if he does move her, you can capture her mid flight.
Conclusion: Queen hunter combos don't need any drillers to get a Queen, unless 1) you want to reuse the queen hunter or 2) enemy has a pirate with drillers to take out your queen hunter

Also they can run away if they have anything that can move the queen at 2x or more speed away from you sub

Ok that makes sense. I'll just have to make sure I'm online at the right time.

If you're worried about your opponent being sneaky, I suggest you do the same - schedule a re-route to some other outpost using your navigator for 10 minutes before you hit their outpost. That way, even if you're not watching, you're definitely not going to crash into his shield and lose your queen killer combo....but then of course, if he's calling your bluff (or just not paying attention), you've move away from a chance to kill him.

There aren't many ways to counter a queen killer - I don't think it's fair to complain that your paranoia that he's going to con you shouldn't be allowed!