My guess? Typically, the translation studios are broken up into the people who actually remove the text (i.e. people who go frame-by-frame or whatever) and those who do actual translation, then those who replace text (like put stuff back on signs). I imagine that the Pokemon team removes stuff with the full intention of "translating" it (or, rather, they just remove it under the general rubric that "everything semi-text-like should be removed"), and then they don't bother doing the extra work to add it back.
Some of these edits are clearly done to avoid controversy, though, which is ridiculous. Fuck Christfags- I was part of that, I know how they act, and trust me, they won't be buying your shit anyway. don't cater to the pissed off soccer moms of the world.