Just hit Tier V mastery on my T6 Jem'Hadar dreadnought, and the ship trait didn't show up. Soon after, I opened an infinity ship trait pack, and that didn't show up either. This happened on my Jem'Hadar character; haven't tried it on any others. With that one, as with all others, any ship traits previously unlocked show up.
EDIT: A while after posting this, I found my Dominion character needed a respec. I did that, and immediately after new traits started showing up again. I'd forgotten the respec bug had been fixed.