This story is not sad, I genuinely have no idea how anyone could think the author would be weird enough to destroy her own story with such a vague or bitter ending when again and again she "attempted" to kill both Joo and Doo...she had the perfect opportunity to do it when Pilwon had the gun or when they jumped over the ledge. That would be bad writing to me because after everything she put them through and for them to die after barely living freely would be pointless and destroy her entire arc for them. I truly know in my mind and heart she wrote that moment as a symbol of Dooshik saving Jooha from drowning like Jooha did for him in the beginning and Jooha gaining his memories back is a perfect moment to give Dooshik back the man he fell in love with after he waited patiently and lovingly.
Sure she could've or should've made another panel showing them resurfacing but it's her story and to me that kiss is beautiful goodbye to us and a welcome home to them.