Okay.
From my experience driving a 52'x15'x8.5' 41ton wood crab boat (1 screw)...
Firstly, if I put it into Neutral, it will disengage from the shaft and stop my screw from spinning. If I put it in gear, even at idle, it engages and turns the prop. Hell, my boat idled at about 4.5knts.
Now will stopping the screw slow the boat faster than leaving it turning? The difference is there, yes. But not worth worrying over. It's not going to instantly stop you either way. Would 3 screws add more drag? Yes, but props themselves aren't that large, and are designed to minimize drag, so it's negligible.
Of course my avg speed was about 7.5knots, not 30knts, or whatever those PT's might go. You will see different effects at higher speeds.
I would be curious to know the dimensions of the PT boat we have, as draft(how deep it sits in the water) will have the largest effect.