There will be fuel in the float chambers at the bottom of the carbs. The main issue would be clearance / access to lifting points when removing the engine - I would say if you are happy they are not in the way or will get damaged when hoisting the engine out they could stay in place. Make sure all the lines and cables going to them are detached before seprtating of course.
The fuel in them will gum up over time. Going over into other angles while engine out may let some of the fuel run into the top end and thin out the engine oil. Given what you have coming up that'll be changed anyway. There should be drains on the bottom of each float bowl if you want to drain the fuel out of them first.
Once you have them off the engine of left on with the airbox off get some plastic bags, or paper towel to fill the openings (venturi?)'s so any dirt or dropped nut, washer etc doesn't go find a new home near your inlet valves or top of piston.
