It might be to prevent two well-coordinated players from playing together and Skyping their strategy (rather than doing it the old-fashioned way over Morse code).
I feel like if coordination is an issue, they could have just made the game FFA only. There are multiple ways to solve the "teams vs randoms" issue, including prioritizing matching parties with other parties. This issue has been solved by numerous other games.
The morse code feature is cute, but I don't think it should undermine traditional communication - through voice or text. Even basic text chat with an onscreen keyboard would foster better teamwork and communication, especially for solo players, or players that are apprehensive about using the 3DS mic. Voice chat is clearly doable, as evidenced in Pokemon X/Y.
I'm really not trying to single out Steel Diver (the gameplay seems very well thought out), but I can't think of another recent team-based shooter (for lack of a better term) that launched without basic party and communication features. BF4 is the only one that sticks out, and the game was laughed at for its lack of pre-game party system. Something like Dark Souls makes sense to not feature overt communication, but it's not being billed as a competitive game.
I haven't played many 3DS games online so I can't say if this is the exception or the rule. I will say that Mario Kart 7 made it very easy to jump in to matchmaking with friends, using a simple queue system. Kid Icarus' multiplayer seems similar in concept (4v4 IIRC) so I wonder what functionality it had compared to Sub Wars.
Sorry if this post comes off as antagonistic. It's not my intention. The issue is just a little worrying to me, considering the nature of the game.