Yes, but even after all that. They never got to talk about what they are, where their relationship stands. True both of them kind of have developed feelings from each other, but its still so ambigous. Especially JK, he only recently acknowledge his feelings to KD. There's still much left in the air.
Thats why, for me, a hug is too intimate for them. For now. The handshake was just right because they are finally ending their deal.

Before shit happened, JK was already thinking if whether he'd ask KD to stay. While he was reflecting on his past actions, he was leaning more on to letting KD go. And KD getting stabbed because of him sealed his decision of letting him go.
Some distance and time apart between them is good in order for some individual growth.A timeskip might be inevitable, however I really hope KD is in a much better place, much better mental state, and economic situation before they meet again. That way, a wholesome relationship may have some chance to grow between them.