If the chimney problem could be cured easily like with cleaning then Mrs. Croft would have it attended to. Smoking Chimneys can be hard to diagnose and fix. Sometimes it is in the structure of the internal parts. I think JA was trying to round out the Admirals character for us. It was actually rude of him to point out the short-commings of the house to Anne-he is unpolished but in Anne's eyes (but not Lady Russells) he didn't mean anything bad by his comments and she takes them in the friendly way they are offered. Many people would have been offended. I expect his wife gave him a little talk on the subject later.