As someone who experiences this kind of issues first hand, removing an item from the shop offer is easy, removing it from the drop tables MAY be easy.
Removing/hiding it from players inventory, keeping track who had it and who didn't and then reimbursing the item is a crapload of effort from developers, sys admins AND QA as it requires separate test build, separate patch, server restarts, testing everything etc.
Long story short: If its not a blocker issue, it can be let there until much easier to prepare hotfix arrives.
Its not even hiding, its disabling temporarly, it appear, but cant be clicked, with an info text "deactivate cause we cant fix a bug bla bla bla", but he still can be bought, etc etc
Every Moba does this when something doesnt work ( hero / item )
And its totally the same with commanders