Seeing in the producer's letter this part: "Additionally, I've already completed my checks for this, but the home base for ninja will be a guild that is located in each city-state and it will be a bit different than what everyone has seen up until now. At a glance it's a building that blends in with the scenery of Eorzea, but it has a different feel when you enter. I was really particular about my checks, and we'll be integrating it very nicely with the lore.", I'm thinking that this may be like Tenshodo from FFXI.

Having a normal store in Jeuno with the store for NIN/SAM downstairs that you needed a special item to get into. Or like the HQ/stores/etc. in Norg for the same NIN/SAM Tenshodo reps. I think it would make sense given how Yoshida described it? Just my guess ^^