Although I think there's a lot of fun stuff in Navis Primer, I do not consider it an essential book unless you want to run an all Ork game, in which case go for it. The expanded Warp Navigation rules are interesting and really well-thought-out, but they turn Navigating the Warp into a mini-adventure run by the Navigator with occasional Charm contributions from other players. It's the sort of thing I'd break out if they're trying a long voyage, but for the most part I wouldn't bother with. There's a lot of good stuff in the Primer, including the new Astropathic and Navigator powers, but it really is a book that focuses on two of the roles on your ship and leaves the rest sort of in the lurch.
Leaving aside the books you have bought (excellent choices), then my next one would be Koronus Bestiary or Hostile Acquisitions. Koronus Bestiary has a lot of fun flavour text entries that can also double as small adventure seeds as they chronicle the adventures of the Galaxy's most patient Seneschal, and then has a Flora/Fauna/Xenos generator in the back so that you have a good framework for creating custom things to try and kill your players. It has some "generic" creatures to run into, and then more specific entries for Eldar, Yu'Vath, Stryix and other Xenos races that you'd run into, plus a few Chaos creatures as well. Hostile Acquisitions has more of a roguish feel to it, and it does have the Nemesis Path as well as alternate ranks and some nice new gear for your players, and it will very much give them more options on how to approach things so it's a really good book for fleshing out the shadier side of Rogue Trading.
I believe that Stars of Inequity has some Tyranid stats in it, as well as a very nice system generator that will help you whip up places for your Explorers to visit, look for treasure and flee from in the span of one session.