I had a Runabout bought prior to the new mission, and it does NOT have the scaling weapons, but DOES have the scaling hull strength, and tractor beam. In other words, the ship was replaced, but none of its equipment was.
Basically, all you really need to do is go to Starbase 39, take the mission, go down to the requisitions officer and trade in the token for a Type 8 Shuttle, strip the new weapons, sheilds, engines and deflector shield off the shuttle, stick them on your Runabout, and delete the Type 8. (Even if you want to keep the Type 8, it's cheaper to buy a second one than to buy another Runabout)
My experience with the scaling weapons is that they are a LITTLE weaker than equipment that is Uncommon or Rare at your level, but comparable to standard equipment. In most cases I was able to improve my DPS by replacing the 360 degree phaser with a turret, but not always. I also enjoyed mounting a 180 degree standard cannon on one.
I also traded the arrays from my Klingon to one of my Feds, so I'd have Phasers on a Klingon shuttle, and Disruptors on a Fed one.
I'd be interested to see if the systems end up placed up for sale on the Exchange, and also whether Type S 360 beam arrays start showing up as ranked weapon types. (You can pretty much put any other weapon on a shuttle in place of the Type S versions with no alteration in firing arc)