They seem to go missing from later incarnations of the ship class, but yes, I'm pretty sure the original model had somebody glue two bona fide "phaser pimples" there (perhaps from the mold that produced the phasers atop the hero ship shuttlebay) and deliberately paint them with the same warning color. Then again, me being pretty sure is neither here nor there.
In closer examination of ST2:TWoK, they don't actually fire phasers, not necessarily.
In Khan's first attack, the phaser fire correctly comes from the sides of the cylinders (where there are single phaser pimples, bracketed by squares of the same yellow warning color even though not covered by it) and wanders further to the sides as the firing progresses. In the nebula, when Khan fires phasers dead ahead, the shot is arranged so that beams starting at the side pimples would line up with the cylinder bows - which are shown glowing bright and steady white throughout the scene. So we can interpret the second firing whichever way we prefer, including the outboard pimples again being the source.
Timo Saloniemi