I still think the coolest way to handle swarm boarding is to make boarders fight the ship itself, dealing exclusively collateral interal damage and receiving damage from the ship's internal acid in return, making it a suicide mission either way. However, this would probably be difficult to implement, and having boarders continously damage the ship's armor would make boarding an extremely overpowered opening tactic, since even the largest hives would get stripped and become extremely vulnerable after a few hours of 1 minute hell. That is, unless swarms still have regenerating armor and it would regenerate faster than the boarders can damage it which means the armor damage is for flavor purposes only (and perpetual 1 minute hell!).
Making them unboardable is a good compromise, making boarding auto-fail is better. As far as identifying the swarm goes, their picture, tech and behaviour are not exactly conspicious, so any player aware enough to attempt boarding during a first contact would probably know what he's up against regardless.