Aye, I didn't miss them at all. I don't mind clickable objects, but I can do away without the need to click on characters to talk to them. That gets slightly tiresome after a dozen or so playthroughs.
IMO they really don't add much. When I discovered the mug I didn't go "Oooh! This was clickable! I wonder what else is!" but rather " Ah, this little bugger was clickable. Hmm, it did felt out of place. Ok." With the cargo, it was even less exciting since there was nothing else to do but click on those. (Though I confess that it took me months before I discovered tritanium has effect on dialogues with Chris).
Last but not least, only fraction of my saves have unlocked first BP because I tend to forget about it (not its content though, that's memorable!)
That would help, but still those objects are tied to screens where you have to click on something. What would work, I guess, is if those screens appeared only if there actually are clickable objects. It would also work as indication players can look for them. As I mention above, I don't particularly like them when all there is to do is click on a character to initiate dialogue.
Ultimately, I agree with Notty's point about consistency.