I agree with you that the most polite reply is simply to return the "good game" or "gg."
Presumably most people who write "thank you" are trying to be polite, though (and in any case it's superior to silence). I did an experiment for a while in which I wrote "good game" after every loss. About 1% of the people I played responded at all, and of those who did respond "hahahahah" was one of the most common replies. So from that perspective, "thank you" is really pretty good.
Chess.com does almost nothing to encourage good sportsmanship (as distinct from discouraging bad sportsmanship), so this is basically to be expected (and anyway, all the other main chess websites have the same problem). I have chat turned off by default now for that reason.
Is "indeed" a good answer to "good game"?
No but it's a good bump.