Could we fully repair and refill any ship that fits inside the hangar bay?

Refill and restocking will be an option, and some degree of repair is possible; the hangar has enough room for technicians and repairmen to walk around the ship and use portable repair tools and onboard supplies to repair damage to a greater degree than a lone mechanic on location in the field, but it's not quite the same as a Crucible's fully equipped workshop. You should be able to perform patch jobs and repairs, but if the ship comes back really wrecked, you'll want a find a proper repair bay or Crucible for a full repair.