Why dock your strike crafts?

Even though I'm disturbed and freaked out by the kissy smiley..

The only time I dock them is when they've gotten so beaten up that they're mostly ineffective (like if you only have 1-2 fighters left out of a squad). Docking them keeps them safe while they rebuild, because otherwise you'd just keep losing the one measly fighter over and over while fighting and the squad won't replenish until the battle is done.

This is only really useful early on when you don't have 50+ squads zipping about, though. Then you just tend to not care about single squads much.

Conceivably, there are some capital ship abilities that make life rather hellish for strike craft but the AI doesn't really use them much (and I don't play MP) so even though docking would spare the craft until those capitals are done, I never had to do it.

I love to have a group of bomber-laden carriers to harass enemy worlds and quickly take out orbital structures.  If a bunch of fighters pop up, that's your signal to retreat.  This command is invaluable for getting your bombers out of trouble, while your fighter squads can continue to cover your retreating forces.

It's useful if you have a carrier-heavy force and you end up being confronted with a flak-heavy force.  Then you just want to dock your strikecraft and get the hell out - your enemy has you countered.  Also can be used when you want to make a quick phase jump out of the system.  Normally you have to wait for all your strikecraft to fly over and dock.  But if you dock them while on your way to the phase lane, there is nothing left to dock once you arrive, and you can just go ahead and jump.

It actually tries to recall the strike craft automatically so that they get back and dock in time if you issue your carriers a jump order, but I'm not sure on the exact mechanics of it (like, if it breaks their current manual attack orders - I know it breaks auto-attack).

It's not perfect on the timing, but it does try

Strike craft do attempt to return, but if the carrier departs first, then the strike craft are magically sucked into the carrier's hangar bay and released when phase jump is complete.

Its fairly obvious when you're in an uncolonizable well with enemy trade ships or scouts regularly jumping in. Strike craft can't resist targeting these guys (unless you've specifically told them not to by turning off auto-attack or set engagement ranges to local/hold) so its entirely possible that a squadron is on the opposite side of the well when the carrier begins charging its phase drive.

Thanks for the insight everyone.  At first I thought this feature was questionable at best but i guess there is a use for it afterall.

I'm still on the fence for hanger bays though.

To me, it looks retarded to have fighters always outside the carrier. The people piloting those fighters must get tired. And the fighters must wear down mechanically. It would make a lot of sense to keep them stationed inside the carrier unless an enemy is nearby.

In fact, I don't understand why sins keeps the fighters and bombers outside. Why aren't they automatically docked unless you ask them to undock or an enemy is near by? That makes much more sense.

In my case, I play Tec mostly.........and that kinda means that in ANY 1 on 1 fight my strikecraft get shamefully decimated. (poor pilots). I have my strikecraft docked most of the time, as I usually have 2 - 3 kol's and 1 - 2 dunnov's in my carrier fleet.

Those caps can wipe out most 50+ strikecraft squads and once I have air superiority(with no strikecraft in the "air") I would launch my own craft. It makes my fleet better distribute damage taken when it counts most.
So even though I take a minor pounding right at the start of battle. The tide can quickly flip when your strikecraft and antimatter run out at almost the same time.

and then they turn tail and die

Well, Advent strikecraft are drones so pilots getting tired is not a problem for them. 

Only time to do it is when you get spammed by flaks since other than a holdout for your strikecraft docking them does nothing.

early in the game I tend to use the dock mechanism when you're coming to a planet with 2-3 flak frigate privateers, I'll then keep 1 out and play cat and mouse with the flaks, while the rest of my ships destroy their mates, then recall and pound the flaks dead

Why bother? Docked craft don't repair any faster. They can't be swapped out for a different squadron any quicker. They can't do a thing to give more antimatter to your cruisers.If your strike fleet is decimated you should be retreating anyway. The only tangible benefit is to spare crushed fleets so that they can be rebuilt without getting shot at. Chances are, however, you need every viable ship on the field, and can't afford to let any fleets be slacking. So no, docking doesn't have much of a direct point to it.

However, docking is good for one thing. You can keep your bombers safe until the enemy fighter screen thins up a bit. This is rarely a benefit though, as there are few deterrents to having everything fielded at once.

Docking your strikecraft manually can also let you phase jump faster since your carrier's won't jump unless your strikecraft are docked. It will only save you a few seconds, but maybe that could make a difference.