So I am thinking of attacking an outpost that the enemy has his pirate at. If I stack subs, can the pirate attack the second one in line and bypass the first?

Indeed

Follow up: let's say the guy with the pirate targets my second sub. If my first sub has a double agent, that will negate the pirate right?

No

What's the outcome in this situation then:

Red Sub one is carrying double agent
Red sub two is carrying drillers.
Both subs are sent from outpost A to outpost B

Blue sub is sent from Outpost B to outpost A.
Blue sub is carrying pirate that is targeting second red sub. How can a pirate pass through the first sub without the double agent doing is deed?

I believe that the oirate can target specific subs, without having to go through the other sub.

However, I think that the pirate would bypass the first sub, hit the second, and if it were to win, go back to outpost A, where along the way it would trip up the DA and convert itself. I think. I really am not sure. The best way is to actually do a simulated test in game, but I'm willing to bet your enemy won't be too willing to help. Maybe another forumer can confirm/deny my thinking...?

If your sub targets an outpost from an outpost, it will interact with other subs travelling along the same path.

If your sub has a pirate and it is targetted at another sub, even if it is on that path, it will not interact with a leading sub.

Like 99% sure. Lol.

The pirate will hit the first sub in its way, even if it is targeting the second.

Really?!? Man that sounds wrong.

Initially I thought you were right, Radio. But I had a weird inkling feeling in the back of my head.

I happen to be in a game with two subs heading at an outpost with a pirate, so I went in and checked. The first sub interacts with the pirate.

It does makes sense, though. The pirate is heading in a straight line, outpost to outpost, even though it is targeting the second sub. I just think we are used to seeing the pirate come from a different angle.
Though, also - if the pirate targets a captured sub of ours sent from the same outpost the pirate is sent from, even in a long line of captured specialists - as we have seen many times before - the pirate will skip the others and go to front, enabling you to recover however many you sent.

It's strange.