I definitely agree and think you should always make time for replying to comments, you dont necessarily have to reply to all of them if you get hundreds or thousands but at least put aside time to read them and then respond to any that prompt you to response as its not really ideal to thank everyone for watching if theres hundreds of comments and some that you dont necessarily have anything to say in response to. If someone is asking a question though or posts a comment which you can respond to with more than a thanks etc I feel its best to respond all the time. I think something larger channels should do is set an hour or two per week to the side so they can sit and read them and reply so they manage their time well.
I honestly get a little bummed out when I write a well articulated and thoughtful message to the youtubers I really admire and get no reply whatsoever. It just feels disingenuous to not make any time for your subscribers. To be honest, to me, it kind of comes off as arrogance or an over-inflated sense of ego. I mean, I know how hard it is to start out on youtube so every little comment or view I get is a blessing and I truly appreciate it when people take the time to leave a comment. I suppose I could see if you were someone like Pewdiepie with as many subscribers as he has but I really don't see why most youtubers can't take just a little time to respond to their fans. One youtuber I really like who is really good about responding is a guy called Weem from weemcast. He's a good example of someone who takes time for his subscribers.
Since, I don't get many comments (2-5 per video), I pretty much reply to every one I get. I'd like to continue this the best I can as time progresses. I want to be a person, not a video-ejecting device.
I respond to all my valid comments, but comments like nice video can you check out my channel or subscribe to my channel get ignored. I can understand larger channels get swamped with comments and just don't have the time to reply and I can't say I envy them in that regard.