Could be that when they upgunned the ship during construction, they had to install power conduits in places not intended to receive any. And just by looking at a starship's main engineering, we can easily tell that the toughest radiation shielding ever devised by man must consist of transparent material; plating or painting it over is apparently impossible...
Only slightly more seriously, I might suggest that those power conduits were indeed a symptom of the upgunning, and that the cover plates for them were temporarily removed because the ship was still undergoing vital testing. A change in the pattern of pulsing lights might give the skipper the seconds of advance warning she'd need to save her vessel from a disastrous malfunction of some sort.
Timo Saloniemi