A means I miss you B means like "yes" or like "어!" or like when you're nodding :) So, I believe B misses A too :)

Haha As a native Korean speaker, I hardly answer 응 back for 보고싶다. but i guess A and B are close friends and 응 kinda means 'me too' a little bit in that context. or B really adroitly tried to avoid to say 보고싶다 back to A. but i guess the former one is right.

In my opinion, It depends on the person. When a friend of mine (we rarely meet) says "I miss you" to me, I prefer to answer him/her with "I miss you, too". I will not answer him/her with "yes/yeah/ok, haha". In my opinion, B just want to says thank you for missing me. Hehe :p. I don't know if it is right or wrong but I hope this will help :)