Quoting tie rule #2 from GC2 Wiki - Ship combat:
If in 50 combat rounds (300 for fleets) the battle is not resolved, the game determines which side is 'tougher' by the formula sqrt( ( 2 * Attack ) + Defense + ( Current HP / 2 ) ). The side with the highest number automatically destroys all opposition.
Doesn't actually say what happens if both sides are exactly evenly matched, though.