" Someone made a conscious choice that these should be labelled, shelved, and sold as boys' clothes."
Yes, but probably the people doing the labelling, shelving and selling (i.e. the staff at the physical John Lewis store) and not the Science Museum upon whom you are heaping shame in your OP...
And they don't just "come up under searches" for girls, they are categorised under Home Page > Baby & Child > Girlswear > Nightwear. So JL online have "made the choice" to list them in the girls category as well as the boys' category. And they are photographed on a fairly unisex child (if I had to guess I'd plump for boy, I suppose, but it could easily be a girl).
I do think it's a significant issue, but it's not a significant issue online. If they are shelved in one area only in the store then that's inappropriate, but you're distracting from that by complaining about the SM and how products are catalogued online.