On some videos like my first lucid dreaming guide (which has over 1.3M views, and thousands of comments) most of the questions are repeated ones I've already answered and the time to answer them is just not worth it - so what I do is I pick certain questions to answer, and also make note of any questions that crop up a lot. If a question crops up many times, I make a video addressing that particular question, and pin the video link at the top of my lucid dreaming guide for a few days.
The rest of the time I try to answer 95% of questions I get, even if sometimes the answer is just for me to point them to a video in which I already answer their question. Some comments slip through the cracks because the way I check my comments is via the email notifications I get, and occasionally if I got multiple messages at once on a video I'll accidentally skip over one or two - but on the whole I reply to most of them, especially on my newest videos.
I also leave my Twitter open to people to contact me there. I've stated in several of my videos that if anyone posts a comment and it doesn't get answered, they can direct message me on Twitter and I'll guarantee them a response. Since I have 14.6k YouTube subscribers and only 150 Twitter followers, telling people to go over to Twitter if they have questions they really need answered makes things much more manageable.