Thanks for the comments, guys.
First of all, the nerfed average earnings are not an intended outcome. As we've said, we will fix those.
As for the "original MO" point - we obviously knew that there would be groups of players with different motivations. Those who want her for the historical aspect, those that want her purely for the earnings and those that care about both. However, not releasing the ship (in any form, whether original or clone) with the original boosted earnings was a requirement so we knew we simply would not be able to make that group of players happy anyway. The reason we chose to do it this way is purely technical - its the only ship which has a modifier built in, so being able to move that into a different area of earnings calculations gives us more freedom to work on the credit economy as a whole, without always having to check whether we didn't break Missouri either way. I'm sorry the chosen implementation might not be fully equivalent at the moment. Once that is achieved you will functionally have the original Missouri again.
Whether it would have been clearer with different naming that the ship has different characteristics - I'm not sure about that, based on observances made around the "B" variants. It's possible, but more likely split down the middle.
There are many purchase motivations, to be sure. There are also many undesirable side-effects of a booster like that: players will overplay MO when they are grinding, causing too many of them in MM at certain periods, credit-related missions and achievements become unbalanced, credit flags become devalued, etc. The original MOs are generally fine, because they are comparatively few and because, as you pointed out, for veteran players they do not have the value anymore. Getting a flood of new boosted MOs would alter the ways those players interact with the game's economy over time and this would be unhealthy for the game.
Also, @Mademoisail meant that that we will adjust the mission for the old Missouri to match pre-patch. We're all a bit tired, since the team is understaffed.
Best,