The judge said New York's law doesn't broadly tax "any and all Internet sales," but instead requires companies to collect state and local sales taxes if the company generates $10,000 or more in revenue as a result of commissions paid to persons in New York for sales referrals.
So, is that per affiliate (i.e. if no New York affiliate generated over $10,000, then Amazon owes no taxes) or aggregated (i.e. affiliates in New York generated $500,000 total payments, and Amazon now owes tax on said $500,000)? My guess would be for the latter.
No. The rule is that if Amazon does enough biz with NY affiliates, it has to pay sales tax on all sales to NY residents. (Of course, it can collect said sales tax from NY residents.)
Your case for wholly-owned warehouses is a reasonable one, and in fact, Amazon collects and pays sales taxes in several of those states.
The New York case is materially different in that it concerns marketing affiliates, not warehouse holding companies.