Granted, I am a f2p player as well, so I might not have all the information. However, I don't believe you are cap'd if you want to purchase more bridge officer or ship slots. At least within reason -- there may be a hard cap, but I assume it is higher than most would care to find.
I doubt I'll ever use 56 Boffs but it's good to know I have some growing room for unique/reward Boffs. I'm pretty much full with just those and a few races I like. Still, I want to have a few other iconic Boffs from the shows/movies.
I've purchased one Doff slot upgrade for 200 total. Nice to know I have some more room if needed.
Ship slots is where I am really curious. I have a ton of nice ships right now and nearly all of the Shuttlecraft, and I don't really want to ditch anything, especially since some will take Dil to replace.