An even Darker SOMA [ending spoilers]

[Cranky Old Man]

The WAU was not on the ark! I won't/don't believe it

If you look at the ark and the space gun neither are visually effected by the WAU. Everything else in the game that the WAU has affected has that look to it, you can tell it is infected.

In the room you first pick up the ark there is WAU in there but it has not infected the woman and it has not touched the ark...

Oh and I took Catherine turning off not as the WAU terminating it but that the virus was working at all systems were shutting down.

Well, yes, and no.
There was no physical GOO on the ARK. However, nano machines are microscopic, and can spread out thin and hide in cracks. They're not always visible, and could easily travel down your arms and onto the ARK.
However, cortex Catherine was visibly infected, and the WAU is even BETTER at infecting DATA. ...so there's no question that if WAU wanted on board the ARK, it would just need to infect Catherine's download with its own code.
...so I'm hesitant to show growths on the satellite hull, but there's a real possibility of WAU spreading within the DATA of the ARK. It could if it wanted to.