I think it depends what the comment is?
Like if you're worried about "oh no! If I didn't reply to comments on my first few episodes, maybe it'll look like I don't reply to comments! ID BETTER GO REPLY TO ALL MY COMMENTS NOW RETROACTIVELY" and the comments are things like "this comic looks pretty i like it" or "oooo intriguing" then.... yes I'd say that's weird. Why are you replying? If the comment doesn't particularly need a reply, it's okay to not reply, and replying months later because you feel like YOU'RE SUPPOSED TO doesn't benefit anyone.
Like, I wouldn't be upset about getting "Thanks! xD" in reply months later, but it wouldn't... really be different from getting no response? The moment has passed.
But if the comment is something like "whoa, where did you get the idea for this" where it's asking a question or "I'm just commenting to let you know this comic changed my life for the better, and here's why" where you really feel like you wanna give them a reply, I don't think there's any unspoken rule that you have to answer all comments in order (as if we were all children again going "she SAID she didn't see my message but I SAW her Like a post on Mary's wall so I KNOW she was online!!") That is dumb nonsense for babies and I won't have it.
If you go back and respond "oh man sorry for the late reply, but thank you so much! Your comment made my day" or "GEEZ SORRY I MISSED REPLYING TO THIS, but to answer your question--" or WHATEVER, it's really not weird, because you clearly had a reason for coming back to answer it!
So TL;DR, my thoughts are: do you actually want to reply to that person? because if you have something you want to tell the commenter, I think it's fine, there's no reason not to tell them. If you are just trying to make it look like you reply to everything, or trying to reply to everything because you think you'll be a bad creator if you don't -- let it go. That doesn't matter as much as you think. It's okay. Just upvote the comment if it's nice and leave it at that!
Re: the footer -- I don't like them, personally, but I've seen a few of them on other comics. I think it's a matter of how you think it reads on your work. My comic tells a story, so inserting a weird ad onto the page sort of awkwardly breaks the mood, but for a gag comic, "SUBSCRIBE FOR MORE!" at the end might honestly fit as a little commercial break. Decide whether it works for your comic!