A friend of mine from off the forums asked a rather pertinent pair of questions:
* "Are we talking about slavery or enforced immigration? Because that's a question of population pressures."
Does the calculus change much if everybody involved starts thinking about the cargo as Beasts of Burden instead of as "slaves?" (echoes of Terry Pratchett: "If it can beg for mercy, then killing it is a crime as far as I'm concerned!")
In both of these instances the method of transport and treatment will have to be, at least on the surface, more humane and comfortable. Lining everyone up, shooting them up with Fast and stacking them on top of each other with a rebreather mask won't work if this is the case. Neither the transporters, nor the customers , are going to experience the same emotional and empathic disconnect in these scenarios that they would with de-humanized slaves. There are some parallels in history - even in the mid-20th Century but I won't go into them here given the forum rules; I'm sure you all know how they worked out the logistics in some of those instances and kept the costs down.
Some crews might be willing to do whatever it takes to cut corners and just get the 'cargo' form point A to B, but that will always be the case. But for the most part if you assume that these are not illegal operations, these two scenarios are going to stem from larger, more public events and markets. As such the buyer will want to make sure his merchandise was handled humanely and was well-cared for, or that the transporters will at least need to comply with any rules and regulations governing the forced (for whatever reason that doesn't involve 'cattle cars') immigration of large numbers of people. Maybe not, but remember that I am going with the legal and open operation here.
Comfy low berths (emergency or single) would be the way to go, if only on the surface. You could put someone in a fake low berth that dopes them with Fast, then take the person(s) out and stack them like cordwood if that's how you think it needs doing. The news people who might take pictures would be happy, the immigrants would willingly go aboard, and the whole operation appear humane with that bit of theater.
As far as the beasts of burden thing goes, are we talking about actual animals or aliens that we think are animals? In the former just shipping embryos or younger versions of the beasts would be better since they take up less space and could be put in appropriately sized low berths for the trip. In the latter case the rules for mere slavery, or better, decent treatment for animals, would apply.
In all cases, the costs have to be weighed on both the market and supplier ends. On the market end there has to be a rationale for providing beasts of burden if robots and machinery can do the same job faster, cheaper, and more reliably. On the supply end you could fit an awful lot of machinery and robots (plus parts) in a hold and with a lot less hassle. Slaves of forced immigration is different, though, since societal factors of prejudice, racism, fear, anger, political or religious reasons and other moral and ethical factors will be tied up in the equation. Expense might be seen and a worthy cost of the operations at the more benign end of the spectrum, or something to be reduced to the lowest possible level and to heck with the drawbacks to the 'freight' on the other end. That is something the circumstances will define.