If you need an NPC to give the characters a boost every now and then, the Warrant and Ship Origin Path from Into the Storm provides some good options under the Contacts heading. These being institutions with which your dynasty is aligned, they could also be people who occassionally come forth with assistance and/or requests of the Rogue Trader.
The ship's Past History could also provide ideas for similar deus ex machina.
For instance, my Rogue Trader's dynasty is aligned with the Adeptus Mechanicus and so they occassionally come forward with "missions" for the PC's. My Rogue Trader is formerly of the Imperial Navy and so he keeps relations with them and gives them a helping hand from time to time. Lastly, there is a Seneschal NPC onboard the PC vessel who is a Quaestor with House Krin, who hold some loans that have been issued to the dynasty. House Krin also issued my Rogue Trader a Letter of Marque, so they have no problems dictating targets of opportunity for privateering operations.
All of these "complications" are set against the PC's own schemes, which are not inconsiderable. Three of our five PC's are constantly cooking up ideas for making a throne. I've found that Rogue Trader is a game that encourages PC's to essentially set the plot by the kinds of endeavors they choose. It seems to require more flexibility from the GM, who occassionally has to account for these things on the fly. Sometimes sessions are cut short when the PC's come up with a grand scheme that requires some unplanned preparation for the GM.
This happened to us recently when our group decided that we wanted to salvage and reconstitute a mining colony that had been ravaged by Chaos Reavers in decades past. We spent the rest of the session coming up with a plan and listing the things that we wished to learn about the old colony, the planet, the surrounding system and any known threats. We then adjorned for the week so that the GM could prepare the next game session based upon our input.