As for Martial Arts, a monk can use monk weapons including the shortsword to make an extra attack as a bonus action it does not not need always be an unarmed strike.
No they can't. The Bonus attack is always an Unarmed Strike
As for Martial Arts, a monk can use monk weapons including the shortsword to make an extra attack as a bonus action it does not not need always be an unarmed strike.
I just reviewed the rules for monks and noticed the following on page 78 of the PHB which renders this entire discussion (in regards to rapiers, short swords and unarmed strikes) moot: "You gain the following benefits while you are unarmed or wielding ONLY monk weapons (the rapier is NOT a monk weapon) and you aren't wearing armor or wielding a shield:". What follows are the bullet points about being able to use DEX instead of STR with unarmed strikes and monk weapons as well as the ability to use a bonus action to make an unarmed strike.
Ahh, good catch. I missed that.
However, you could still draw the rapier if you wanted to shadowstep, attack, attack on a turn. Then you could sheathe it on the next turn if you wanted to attack, attack, martial arts (x2 shortswords now).
But yeah, it's not quite as good as I had originally thought.