You'd be advised to add something to add some KH back to the water. That can be a passive source like crushed coral, or something that can be dosed like baking soda. Getting KH up to 3 or thereabouts would be beneficial for a few reasons.
Your fish gasping likely isn't related to pH that I know of, but to high CO2 levels.
pH WILL affect whether your filter bacteria work, however. When the pH is lower than about 6.4, the ammonia your tank produces stays as ammonium (which the filter bacteria can't consume). At 6.0 ammonium isn't immediately deadly, but if you shut your CO2 off and the pH goes up to 7+ right before morning, that ammonium will change back to ammonia and is toxic. This is also why even if you add baking soda don't do it all at once, and when your pH is at 6.0. Do so in the morning when I suspect your pH test would read above 6.4.
Trying to keep a stable pH at very low KH values is very difficult, since there's no resistance the change.
You're not using a pH controller, are you?