There is a mass transit system, it's described in my latest RP, I feel somewhat embarrassed about not putting it in sooner. It criss-crosses the entire ship, and underlines the entirety of the city.
As this was a city I didn't think that writing about ever sky-scraper and are of accommodation would be worth it. As shown in the description of the Destiny, they are present, and dominate most of the city.
As for an armory. Most of the population of the ship are colonists, and a good proportion of them are Nepleslian. You don't want to give them easy access to weapons. Therefore there are armories and weapons lockers in the areas where the crew and military forces live. There are also weapons lockers around the ship, but they're protected from casual access.
As with boarders, it is not that easy to reach the Destiny. It's gravitic shield is extremely powerful, and very few ships could reach it, and this is while it's escort ships are blasting at it. I'm sure it could, and likely will happen, and this is why there are internal security systems, automated drones, and the security forces.
I didn't really think of a jail. I suppose if might be needed, there are Neplesians after all. There will likely be a single large institution which can serve the purpose as wither a detainment centre, where you can hold someone for a short amount of time, or a long term prison and re-education centre. Or it could use the more draconian StarArmy system, not that used on Neplesia though, the Destiny isn't like that.
As for cars, trucks and roads, I'm not sure. I was thinking pedestrian streets, if you need to go far you can use the mass transit system. Large load, construction duty etc.. would use a more heavy duty version of the transit system, and would likely get drones to do it.
Under the job category, although we could simply have drones, such as the NovaCorp construction drone, to take care of it, I see that having a job like this might be beneficial, so maintenance duties might be spread between the drones and the colonists. The engineering corp. will take care of all the really major events, with the help of the AI and drones.
Thank you for the advice.