I really don't see the big deal about the Joker "missing" Harley. So what? Joker's idea of love and missing someone is totally different than the normal person.
The only "love" shared between the two was when they were reunited. And even then originally he was meant to push her out of the helicopter.
He bailed on her earlier in the movie.
This was after he used her to psychologically torment his prey.
If you remove the gangsta song during the chemical wedding scene and just hear the cords/score and see the conflicted look in eyes its great stuff.
It seemed clear that Ayer's Joker is the type who is only afraid to be in love Harley . However, he consistently loves to control her.
There is a gap between him leaving her in the water to trashing his place in a very "Pink Floyd" kind of way. About a year or so with her being locked up.
You don't know exactly what made him get that low, but he's there. He can't control certain things like he use too. (Doesn't help they edited down his part and are trying to establish the Joker's history while keeping just a subplot in the film)
I think Joker loves Harley, but not in a traditional way. He loves the toy. He loves her like a pet. He got to use to it being around him so much that he's not use to being without it. Harley just sees some form of love. That's good enough for her (at this time).