First....I just have to say this is a brilliant idea and I have no idea why I have not seen this attempted anywhere before now. With that being said, on to the answer:
First, to end any speculation about throwing weapons:
"...If a weapon has the 'thrown' property, you can throw the weapon to make a ranged attack. If the weapon is a melee weapon, you use the same ability modifier ... that you would use for a melee attack with the weapon..."
So yes, Thrown weapons are melee weapons first and foremost that CAN (or can not) be used to also make ranged weapon attacks. They are not ONLY ranged weapons, like the bow and crossbow; found in their own Ranged Weapon table.
Lastly, yes, because monks are proficient in Spears and Javelins, and a 'Monk Weapon' is any weapon the Monk is proficient in as well as Unarmed Strikes; Spears and Javelins DO benefit from the 'Martial Arts' bonus and everything included under the 'Martial Arts' class ability. Including being able to make an unarmed strike as a bonus action when you use the Attack Action to either throw a Spear or Javelin or attack with either in melee combat.
On the note of Dual Wielding; be mindful that you can hold a Spear or Javelin in both hands if you really wanted to; but the rules on Two Weapon Fighting (Dual Wielding) require both weapons to have the 'Light' property before you are able to swing with BOTH in the same turn; unless you have the particular feat that says otherwise.