I'm the kind of person who would be annoyed by such things, but the utility of the extra queens trumps any sense of disorder I have about them. I would be far more upset about having to improvise the extra queen when it's needed than about having pieces that are out of place.
Think of them like spare buttons on a shirt: they're typically sewed into it in an inconspicuous location. Find an inconspicuous location for those queens (where the kids can't see them) and be thankful you have them.
First, I recognize why they now put an extra queen of each color into nearly all chess sets. Because especially with short time controls, those queens need to be at the ready in a tournament.
But I still don't like them. It somehow ruins the completeness of the chess set. Dump all the pieces out and you have these two awkward pieces left over. What to do with them?
My little kids are baffled--nay, upset--that they don't get to play with all the pieces. It's actually hard for me to explain to them why the extra queens are there if you don't get to play with them. I've taught teenagers how to play, and they get hung up on it, too.
And now I'm hung up on it. A chess set (board and pieces) should be a complete thing, a harmonious whole in which every part is used. Setting up a chessboard is a neat moment when it all comes together in an aesthetic in which everything has its place.
I grew up without queens in my chess sets, so maybe I'm just getting old and crotchety and complaining about change. But I have to know: is anyone else bothered by the extra queens like I am? Does anyone else care?