This one is weird. The search text is not visible in my Atom 1.25.0 x64 on OS X 10.11.6. I’ve dumped a screenshot here. The search functionality is working though.
I have disabled all addons, removed all custom css, even reinstalled Atom completely. I even reinstalled OS X (for other reasons) and thus reinstalled Atom. Same problem on a brand new clean machine!
I have seen this behaviour also in the file rename modal, but cannot reproduce this. After two times renaming, that behaviour was back to normal.