You can quite happily spend an adventure inside the ship. Hell, you could run an entire campaign inside the ship if you really wanted.
If you have a barracks component, you can expect to find squad, platoon and even company-strength combat drill going on on a daily basis. The reason barracking for a regiment takes up more space than quarters for 18,000+ crewmen is training space and military stores, allowing the regiment not to suffer in combat readiness during a month or more in the warp.
See Priests of Mars for some real shipboard combat environments...essentially modular, reconfigurable 'cityfight decks' complete with servitors carrying soft-slug autoguns. Also for some good looks at the engine decks of a major capital ship - complete with asteroidshine* stills, scrap-metal shrines to the Emperor or Omnissiah, and bits of tech left over from and forgotten by previous crews.
Vermin hunts through the machine spaces will be a continuous thing; every so often the Arch-militant may be asked to support a Ghilliam (betweendeck mutant) hunt.
Somewhere in the command or cargo decks there are almost certainly hidden treasures if the ship's been in Dynasty service more than a few centuries. Unfortunately, if the crew find the invasive archeotech devices first....
For that matter, the existance of 'voidborn' as an origin implies communities other than simple barrack quarters. Whilst the population is far from self-sustaining, if half a percent of the crew of a Vagabond-class merchant were to find a partner and have a single child over a decade, that's still something like a hundred children somewhere on the ship that the Lord Captain, as feudal liege, has some level of responsibility for. It's not unreasonable that they might end up assigned to their parent's watches, but a Rogue Trader with his eye on morale - and not wasting talent - might well identify the sparkier ones and see them trained up as more meaningful crew than a chain-hauler.
For that matter, gang/territorial rivalries can be imagined - especially between groups that are divided into factions by the ship's crew structure; the crews of adjacent guns in a macrobattery, for example.
Equally, whilst a Rogue Trader has the option to draft in prisoners to replace crew losses at a world which allows him to, in addition to the morale loss, there's also the risk of picking up some real bullies or criminal hard-cases. Before you know it, you've got black markets and protection rackets rife in the crew quarters and working decks, and the armsmen are having real trouble maintaining order. If you really want to earn the respect of the crew back, a Rogue trader, Seneschal and Arch-Militant could consider going undercover amongst his own crew (because seriously, how many of your city's council members do you know by sight?) to deal with this problem before it impacts the running of the ship.
Lastly, the post-battle (and during battle) narrative becomes a lot more emotionally involving if there are NPCs the players know and give a damn about on the ship. Trying to get past massive damage to the ship's structure to reach the deck where the aforementioned children are trapped is a worthwhile mission in and of itself, and worth several points of morale if the explorers are prepared to risk themselves in the attempt.
In a game I've GM-ed, the players knew the Astrographer and his aides in their observation dome and librarium quite well, as they tended to be the 'voice of the GM' when it came to plot exposition on the system they'd arrived in. When the dome was hit by a lance shot and the adjacent librarium caught fire, they were genuinely hesitant to respond by depressurising the deck, because they knew it would involve killing them.
Babylon 5 'downbelow' and/or the dockworkers episode are very good sources of inspiration.
* "Like moonshine but a lot rougher and with significantly more caustic chemicals in it"
Edited by Magnus Grendel, 20 November 2013 - 09:20 AM.