Here's a potential solution to consider:
Turbine adds a fixed location on the top deck for the ah, mail, bartender, bank and guild chest for all ships. These areas are initially blank, with no NPCs to click. As players, we have no ability to re-arrange them; only turn them on or off.
If you place the corresponding newstyle buffs anywhere on the lower decks, the top deck versions "turn on." As in, if you place the Orien Express, the ah, mail and banker on the top deck become visible and usable. If you buy and place the banquet hall, the bartender shows up. (The banquet hall specifically, because that's the buff that turns the entire top deck into a tavern area.) If you buy and place any guild chest, that specific guild chest appears on the top deck.
One key element is that all five of these top deck NPCs should be close to each other, located in the same area on the top deck. Specifically, the area where the buff bar is. No running up and down ramps or turning corners.
If this were implemented, I'd switch my vote to "turn off the cargo hold." Without this, my vote remains to keep the cargo hold as-is.
EDIT: Actually, one more thing: I will be most unhappy if/when we lose the ability to put a stone of change on the ship. This is currently only possible in the cargo hold.