They don't show up for me, even after fixing them, maybe it's bugged or BW just thought nobody would notice.
Anyway... in the Ord Mantell cantina, there's a song on the jukebox called "For the Republic", I think I recognize it from KOTOR. The same track also plays when doing the bonus quest in Sobrik, when you have to reprogram the imperial cantina sound system.
Oteg mentions a Republic ship named Onasi in Maelstrom,
During one of the early BH quests on Hutta you can mimic Calo Nord with the countdown thing.
The "Knight of the Republic" title of the JK may be a not-so-subtle reference too.
During the Consular story there's an ambassador/senator guy from Manaan in your ship. Also all the Kolto abilities.
The high-level Guardian helms may be modeled after the headgear in KOTOR, both are goggles/visors of some sort.