Nice report, fabulous museum.
If you ever get the chance you should try and visit its counterpart in Rio de Janeiro, the Museo Naval. It covers part of the same territory but with the focus on Brazil naturally enough.
There's also a small but fascinating little museum inside the Farol da Barra (Forte Santo Antônio) in Salvador, the Museo Náutico. If you ever do go, do take the walk up the hill to the British Cemetary, there are a number of RN interrals there.
A few years ago we rented an apartment for a couple of months in Larenjeiras in Rio. One of the streets that runs through the adjoining neighbourhood of Largo do Machado is Rua Gago de Countinho, named after the Portuguese aviator whose aircraft sits in the Lisbon museum.