Sometimes, when you use the word 'subscribe' in a comment, YouTube might put that comment in the 'held for review' or 'likely spam' folder and it won't appear to the public in the comment section. However, that is when you comment on other people's videos and I don't recall it ever happening on your own channel/videos.
Replying is important, people like to be recognized or acknowledged but they don't like advertising and promotions. If they see you copying and pasting the same reply to everybody, now they realize that your reply to them was not special. Especially if they commented on several videos and you replied with the same canned message each time.