I have Katja and Dogmeat as companions but they constantly hit for no damage. Is there a way to change this? I already gave her a submachine gun but she insists on using her knife.

It depends on who or what you are fighting. Any one in power armor or super mutants will have a high damage threshold and will suffer less damage from all attacks. Dogmeat only has teeth which don't do a lot of damage, and Katja has a much higher melee skill than small guns skill so she will default to knives. If you want some gun toting companions try Ian or Tycho.