Aren't we forgetting a crucial modification from the very beginning? Janeway's personal dining room (top officer dining room?) was converted to Neelix' galley in "Phage"...
On a similar vein, "Parallax" introduced the hydroponics farm, and "Elogium" the airponics version. Both the galley and the food production facilities no doubt introduced some technologies and techniques not previously known to the UFP, even if these were a bit more modest in scope than the isokinetic cannon.
As for the transaction on said cannon, yes, the episode confirms that it proceeded. Then again, the Entharans were said to be very strict about the way their citizens handled interstellar business. If they found something amiss with what Kovin did, they might have forced Janeway to return the cannon and undo the deal, as they wouldn't want the word to spread that their world was involved in shady deals even if the customer was completely satisfied.
Then again, the Entharans might have best protected their reputation by letting the transaction stand. So perhaps Janeway kept the cannon, but didn't use it much, probably because the installation was said to require specific software settings that were out of the ordinary. The ship might not have functioned properly with those settings, or Kovin might not have had time to finish inputting the settings.
Timo Saloniemi