Arstotzka has been using fireballs at sea the entire time.
However, their ships have the trade off of being worse at combat but having a higher bonus when landing troops. Moskurgs needed to develop research to do sea magic likely as a balancing mechanism - once they did things began tipping in their favor. Once Arstotzka shifted their ships back into one massive fleet, things became balanced again.
That ... doesn't exactly address ebbor's concerns. So all this time our ships have been worse at combat than Moskurg sailing ships? That wasn't mentioned in the opening post of this thread, where it was stated that our ships are slow, but can carry lots of troops. Nowhere was it stated that our ships are strictly worse at combat than those of Moskurg. A reasonable interpretation of this would be our ships are strategically slower to move from port to port than Moskurg, but as rowing ships are more manoeuvrable than sails, the two should be about equal in combat.
Again, Moskurg is receiving the advantage (better combat ships), whereas our advantage of landing more troops doesn't even apply until we've captured the whole coastline, which we would be hard-pressed to do given the Moskurg advantage. And again,
none of us would have known this without you mentioning it, since nowhere is it stated that our losses at sea were due to our ships being worse at combat than those of Moskurg.
Overall,
all this salt is coming because we have introduced several new things in the past two turns, where Moskurg has introduced none, and yet combat has not shifted an inch in our favour. The only possibilities are that Moskurg has developed some incredibly powerful and incredibly subtle magic that shifts combat, which is beyond your ability to reasonably describe or hint at without giving it away completely, or that we are not progressing because our designs don't address the mechanical reason why we're not winning, which is again due to the descriptions not adequately matching the underlying mechanics you're using for rolls.