One of the reasons a lot of ships don't make sense in Traveller: they are here for gaming. While I do like ships to make sense, it is more "what sort of adventure can this ship provide us". I spent a LOT of time way back designing really horrible ships simply because it was fun. I have no idea how many deck plans over the decades have been doodled out that, from a real-world perspective, make zero sense.One problem with this method is reliability of the transport ship crew (scenario time for gaming). There could be several versions of this. The transport ship is contracted to take the prisoners to planet / system X. They load up and then disappear. This could be for various reasons including:
Payoff of the crew by one or more of the prisoners or their not in prison associates. Here the prisoners include members of a gang, cartel, or other major criminal enterprise.
Same scenario only enemies of one or more of the prisoners want them.
The crew knows where they can get a big reward for showing up with one or more of the prisoners.
The ship is a scheduled transport rather than a government run ship that can be kept off public records as to when and where it's going. Here, the transport arrives and... PIRATES! Bad guys jump the transport because they have a pretty good idea where it will be and when. The crew having no motivation to retain the prisoner module jettisons it and runs. The pirates only want the module anyway.
Anyway, this is less likely if the ship is one where everything or nothing arrives, not two separate pieces. It would help immensely that the crew were professionals that had been fully vetted and are motivated to do the job correctly and honestly.
Escape is more likely to occur with outside help than by the prisoners themselves. Among the prisoners you'd need some that can run a starship for starters. That might be a tall order to meet.
Sort of like the ever-present dungeons in fantasy games: the environment and creatures lurking about usually make zero sense from a habitat point of view, they are simply there for the adventure.
Though that is really changing I feel now, based on a lot of the things I read about dungeon creation. So perhaps Traveller ships can start to make more sense, as pointed out by several people here (and a shout out to Spinward Flow's extensive thought experiments on ship design, as well as several others who also work on "practical" ships). Though I'll just keep with my badly designed ships because that is how I have fun.