The problem with just ordering online is that no one will then encounter these books unless they are specifically searching them out. No one will pick up a copy of Material Girls or Hags or Time to Think or Irreversible Damage or Trans or similar books, because they won't even know they're being written. Instead you see entire tables devoted to trans issues, but all from one perspective. If you aren't already paying attention to this issue you therefore may never even realise there are books to be bought.
And from the bookstores' perspective, if everyone is just ordering online, then they can justifiably say that there is no demand so they won't order any copies in.
I don't believe their claim that the books just sold out quickly as well. I went into the Victoria branch on the day of publication, and every few days after that, and they neither had copies nor would allow me to order into the shop - they just directed me to the Kings Road branch as Picadilly, Hatchards, and Foyles (owned by Waterstones) all had no copies.