Functional changes in coloration are much "easier" (read: more likely) to develop through random mutation than functional changes to complex mechanical structures like bone structure or musculature. Given their predecessors were already under selective pressure by predation for millions of years prior, it's reasonable to assume they'd developed countershading (light bottom, dark top). Plus current agnathans are usually pretty dull.
Edit: oh geez, I misunderstood your message. It totally could have been a rainbow party blimp. That mostly depends on what their habitat was like.
Of course! I'm a biologist, I try to use my powers for good.