I've stabilized myself with a bomb way off the stage to give me time to throw out a missile, and I've managed some stuff like edgehop into missile or edgehop into neutral B for a quirky "**** off" type of recovery.
Don't rely on Samus' shorthop for your combo game. She's got one of the worst SHFFL games of the cast, and your combo game should ideally be ground-to-air or incorporate platform play in a way that you can work around Samus' shorthop drawback. She's got an incredible wavedash and a solid waveland, so using those for your approaches should be more of a goal than SHFFL game is. Her shorthop does get more comfortable as you play, but it gets more comfortable in the sense that you know how to use the stage around you to avoid having to bust it out. There are applications for her shorthop, like an empty shorthop into a waveland, but other than that you'll be playing a heavy ground-to-air game when it comes to comboing.