I thought Hook sounded concerned for Emma, and trying to reassure her. It was a contrast to the way Grumpy/Leyroy sounded sort of insensitive about it.
Then again, he’s supposed to have “missed [Bae] very much” but we haven’t seen much of that side, more the “rival rival rival” mode for the most part. If he said “I hope he is safe too” or “I am sure we will find him .” or even better both, “I am sure he is safe and we will find him”–THAT would be very nice and show an affirmative desire that Neal is safe. This way its like a deflection, “Turn up” makes him sound like a bad penny you just can’t get rid of, but the tone was not sarcastic even if the phrase chosen could have more strongly told us that Hook cares about Neal for his own sake. Instead, it seems this was more said to reassure Emma for her sake, because Hook cares about her, even if he doesn’t care or even doesn’t much mind if Neal doesn’t turn up.
“If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn't. And contrary wise, what is, it wouldn't be. And what it wouldn't be, it would. You see?” -- Lewis Carroll, Alice's Adventures in Wonderland & Through the Looking-Glass