Great question and it made me think. I use "indeed" very infrquently and as a "filler" word, trying to get the other person to explain more about their issue. In fact it is a bit like the japanese "hi" or "yes" so very non decisive. I also use it as a question with a rising inflection for the same purpose. BTW (by the way) it is years since I was in Japan so my knowledge of "hi" is very rusty. :-)

yes

Thank you so much! It was very easy to understand!!

its probably most similar to the word "certainly" (which is more common and fine to use). Its not commonly used. I think using it to agree with someone could seem a little odd in regular company. When I picture that word being used I think of professors talking to each other so I think it could be a bit overly formal in certain circumstances.