If I'm not mistaken, the Reaver version that crashed at Mr. Universe's place, was the only physical model ever built. that version had all the markings obscured to hide itself when escaping Miranda. That's why Inara was repainting it at the end of SERENITY,
It's the only physical model they built, but all previous shots with the CG version of the Reaverized ship had the logo still on there
There was no reason to remove the logo anyway, not like the Reavers would care, and the Operative already knows who they are.
The logo is also missing from the shot where they dock on Beaumonde, though that's probably because that shot was done by a different FX studio that specializes in matte paintings.