Shouldn't there be a phaser emplacement where Mandel suspected the ion pod to be located?![]()
Perhaps - but apparently also at the exact intersection point of the beams in the image you linked to, which would be the ring above the ventral dome, to port and thus just behind the dome when viewed from starboard.

Seriously, forks, having a phaser emitter (capable of spitting out two beams) at the bottom of the dome plus at each of the three little pimples on that ring would nicely account for the existence of four distinct phasers, enumerated in "Paradise Syndrome", firing twin beams from the general area of the lower dome. If the ring rotates, we have a number of firing angles plus a Gatling action of sorts to take care of the unfortunate overheating problem of these weapons ("Balance of Terror"). And a tetrahedron of emitters is an appealing geometry in many ways.
Then again, the "Gatling ring" would make the existence of things like starboard phasers somewhat redundant. And we have seen that the aft phasers of the Defiant weren't on a Gatling ring around the dome atop the shuttlebay. And the top saucer dome lacks rings and pimples of any sort...
As regards the ion pod, many a thing was left unexplained and may safely remain so. But the idea that the very existence of this pod would pose a danger to the entire ship is quite an absurdity that transcends the McGuffin nature of this pod and yells for an explanation. Yet we get none - even though the plot hinges on Kirk being accused of jettisoning the pod. How could he possibly be blamed for this action even if it cost the life of Finney? If so much is at risk, then a few fumbled warnings or mistimed keypresses should not lead to a murder charge, merely to an inquest and reprimand for carelessness in handling a deadly crisis. And Finney could be buried in absentia after being stripped of rank and publicly disgraced, for having had the indecency to die in a way that jeopardized the safety of the ship.
This is the main reason I prefer to think that the pod posed no danger whatsoever, and had to be jettisoned only because this was the way to get the ship out of the danger posed by the storm. Kirk would have had options, then: jettison and escape, or not jettison and escape. The former would get the mission accomplished and justify the damage and risk to the ship; the latter would mean embarrassing and expensive mission failure, but at least Finney would be alive.
If Kirk were committing premeditated murder here, and the pod itself posed a risk to the ship, the charge should not be one of jettisoning Finney to his death. It should be choosing a particularly monstrous means of murder that threatened the lives of 428 innocents. If the pod plays a minor role here, merely being the murder weapon, then the approach taken in the trial is fully justified and understandable. It all deals with whether Kirk jettisoned Finney in an understandable accident or in sinister murderous deliberation, after all, never touching upon the wider repercussions of the act.
Timo Saloniemi