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I tried to send newly captured pirates from away mission to colony base via transpord pod but that resulted in them losing restrains. They just become hostiles wondering around without any program to do anything. My pawns cannot take them to prisoner room or arrest, only shoot to death. I expected them to be restrained and keep their prisoner status as it was when they were placed in the transport pod.

I found the same reports with answer the bug was fixed:
https://ludeon.com/forums/index.php?topic=46175.0
https://ludeon.com/forums/index.php?topic=45915.0

...but obviously it was not:
https://ludeon.com/forums/index.php?topic=47938.0

Also, I have no mods.

Well, I tried sending some captured pirates from away mission map to my colony base via transport pod and found out they lose their prisoner restrains in the process. It results in that they are showed as hostile, not as prisoners. These hostile pawns do not have any program to attack, fight or retreat, they just wander around doing nothing, like they do when caravan stops for random encounter. But I can't make my pawns take them to prisoner beds or arrest them. Only shoot to death. I figured out it's a bug and wanted to report it just before but found the same exact two reports with answer the bug had been fixed:
https://ludeon.com/forums/index.php?topic=46175.msg438995#msg438995
https://ludeon.com/forums/index.php?topic=45915.0

So, my question is: is it only me or someone else still has the same problem.

The insterstellar dust would eat up the armor/hull and destroy the ship.

That is quite an observation! This inerstellar dust will act on spaceship as water does on submarine applying friction and reducing ship speed. I fear that this friction will counterbalance propulsion force long before relativistic factor becomes long enough to be sufficient. On the good note now we found how to replenish our evanescent matter needed for propulsion system!

Pawn with social skill level 16 has 24% trade price improvement. Trade inspiration can add another 15%. Buying factor is 1.40 and selling is 0.60. After applying pawn's skill and inspiration they will become 1.40 * (1 - 0.24 - 0.15) = 0.854 and 0.60 * (1 + 0.24 + 0.15) = 0.834. At least you can buy items cheaper then their prime cost effectively increasing your colony wealth. And this is not the best case. There is 2% bonus when your caravans trade with other settlements. Unfortunately I don't know how much trade inprovement skill 20 pawns have, but I hope I will know soon as my fast learner great memory one-fire tradeswoman train.

...it only had 4 hours left before bleeding out, and I couldnt operate on it... It just kept wandering around without one...

For emergency purposes sleeping spot will work just fine.

... So you'll need to vaporize 10^6 kg of matter to get to that speed.

Energy conservation law is not the main wet blanket though. Momentum conservation law is. To get some speed one need to push off from something. Rockets push off from reaction mass and this is where all the matter is squandered away. The best engine in terms of matter-efficiency is ions thrusters which will expell ionized atoms at sublight speed but their propulsion force will still be very low.

At the speed of light, people on a rocket will look out their window to see time seemingly stopped. And when they reach their destination, it doesn't matter how many centuries they traveled, they wouldn't have aged at all.

No, that is not what will happen. When they look through view port they will see the world will shrink into one point their rocket is moving towards. But that is just optical illusion due to relativistic Doppler effect, what they will see after applying some correction calculations is that the world is flatten across direction of their rocket speed vector (Lorentz contraction) and they threat a lot of real distance just like that.

But their time will not stop, they will age just as every one else given that their journey is long enough. And it must be long enough, I can guaranty that as I some time have tried to calculate time in rocket clocks which is needed to reach 90% of The Speed Of Light travelling with safe acceleration. There is also time needed to reach destination and this time is not some short timespan.

What a mess! Joules and Newtons are two absolutely different things! To convert energy into force you need a coefficient that reflect propulsion system ship is using. And there are so many things to consider including speed at which matter and antimatter is converting into energy.

Also one cannot reach The Speed Of Light. Never. The closer you get to it the less acceleration with the same propulsion force is. Also there is time dilation thing. For wingside spectator rocket will lose propulsion force as its time slows. But nevertheless that just for some unrelated people, rocket passengers will see the same problem just from another angle because of relativistic factor:

F = dp / dt

p = γ m v

γ = 1 / (1 - v^2 / c^2) ^ (1/2)

a = dv / dt

Now in case F || v:

F = d/dt [m v / (1 - v^2 / c^2) ^ (1/2)] = m dv/dt / (1 - v^2 / c^2) ^ (3/2)

And:

F = γ^3 m a

a = F / (m γ^3)

So the greater the speed v is, the greater the relativistic factor γ is and the less acceleration a is.

Every type of sleeping spot (including that for humans) have there modifiers for rest gain, immunity gain and surgery success. You want your dogs haul more and sleep less? Give them better bed with rest buff. You want your muffalos heal the plague faster and not to die? Give them better bed with heal and treatment buffs.

Also be wary: sleeping boxes do not admit large animals like muffalos and dromedaries, but they easer and cheaper to build. Also calves of said animals can still sleep in them until they grow up.

If you like it's being fun try playing with Phoebe. There will be peaceful times but every now and then events will pour down on you like from the horn of plenty. Thing will become really hectic. This is much more interesting that Cassandra's fixed frequency evens that are like bum...bum...bum, very annoying in my opinion.

...I think a good deal of it may be that I got several large manhunters packs (elephants, rhinos, boars) and a LOT of food as a result...

You should have kept the meat in the form of corpses, especially the large ones like rhinos and elephants. In this form meat and leather will not increase your colony wealth as well as save A LOT OF space.

Food poisoning due to low cooking skill and/or dirty cooking area apparently. Does bionic stomach makes pawns immune to such misfortune?

The description of bionic stomach suggests that pawn with one becomes poison immune. Is my conjecture true?

...I also almost never travelled because it was super slow...

Now try settle somewhere on the road near cluster of settlements preferably not in jungle or mountain area as these terrains greatly slow down caravan moving speed. You will get a lot of trade quests which will bring sometimes very unique items.

Later in the game you can use moisture pump to convert marsh and mud into farmable soil. In the early game you can use bridges to make such tiles buildable. Presents of marsh cells on the map is integral part of biome you have chosen, so the only way to reduce amount of marsh is to try another world tile and see if it will be placed somewhere near the edges. But make double sure that you choose exactly boreal forest and not some cold swamp.

Also there is such information as overall rainfall for every world tile. Try selecting one with minimal possible value. Not sure if this helps, but there is no harm in trying.