ship upgrade does not affect anyother person but yoursellf, as its an upgrade for a MINI game.
They have stated that they are working on a major overhaul for the space combat portion of the game. While they haven't said how, there have been innumerable threads about space PvP and group space missions and so on. So while ship upgrades only affect you "right now," in the future they could affect a lot more than just you. So I would agree that ship upgrades should not be part of a cash shop.
That said, I'm also against the idea of a cash shopt for the game. If the shop sells anything other than vanity items, that would be the end of my time in the game.