The staff (not the dinosaurs) at Henn na Hotel Tokyo were extremely helpful.
Provided there's space, there was no issue with just hopping on the Disney shuttle without a ticket, and when we had to extend our stay for an extra night we were able to check-in to one room early.
The metro is a short walk away and connects to major stations making getting around Tokyo on a 24hr ticket simple (you don't need a ticket for 4yr olds)