Hello would appreciate if someone can help me with this.

My enemy has a sub with a pirate, nav & assassin but no drillers, which he has sent to intercept his ally's sub but pass over where my queen is - clearly with the intention to turn at the last minute to me.

I have a pirate at that station and want to pre-empt this and therefore steal his specialists but don't seem to be able to target the sub with the navigator,

Are pirates not able to target subs with navigators on board?

Thanks

Yes, they can target them, however if you set the pirate onto the navigator sub and it switches direction, your sub will try to follow it, often times doing the "pirate glitch" and trying to run all the way around the map in order to follow the navi. So, if you plan on pirating a navi, make sure you do it at the last moment, and hope he doesn't change directions.

Good luck!