I think "Miss na kita" simply means "I miss you."
"Miss na Miss kita" means "I miss you very much" or "I miss you so much"
"I already miss you" means "Namimiss na kita."
We repeat a word to put more stress in it. Unlike English, we can use "very" or "so". In Tagalog, we don't have these words so we use words repetitively.
Another example would be:
Gusto kita- I like you.
Gustong-gusto kita- I like you very much.