Over at Twilight of the GM there's a good post on low cost travel. I'm more interested in the Working Passage section. I'm assuming that most Traveller players are familiar enough with the risks of low passage, and quite honestly, IMTU there's little need for stowaways from able bodied workers.
He's got a good point that most spacers seeking working passage are going to be rather down on their luck, and really the Loneliest Man on the Ship. He's not part of the team that's the crew, yet he's not part of the passengers. In frontier and unsettled areas, a man working his passage is really a quasi-legal form of slavery. Limited in length, but there's little, if any, redress possible to the Captain's authority. Good captains are not going to have much of a problem with crew retention, but sometimes there may be issues in the crew that require a spot correction.
Also, I am of the opinion that in most universes for Traveller, there is going to be some sort of Hiring Hall or Guild for Starfarers in decent sized ports. Perhaps along the lines of modern maritime unions, or maybe in the model of the Worshipful Company of Shipbuilders or Honorable Company of Master Mariners. Generally, rolls for people looking for Working Passage should be based on Technology Level and size of the port. A guild member in good standing would be more likely to be trusted than some random spacer looking for work and desperate to leave, and only recommended by charitable organizations. If a guild member is mistreated by the Captain, the Captain can receive penalties the next time he stops at that port, or possibly loose his own membership (mistreats brother spacers!). This is a way to cover from a player missing from the session.
If the PC's are operating a starship, you can also use Working Passage to introduce characters like a Rhysling, or a older, semi-retired spacer, who perhaps is a contact of one of the crewmen, and takes Working Passages on a few starships with good routes to see the universe. Working passage, spend a while on planet, and then look for another to get home, or keep going, Think of the old James Garner movies "Support Your Local Sheriff!" and "Support Your Local Gunfighter" where the hero is going through to somewhere else, or Lazarus Long at the time of the "The Tale of the Adopted Daughter" . If they turn out to like the old codger, there's a ready made adventure hook.