Both the props/shafts and the bronze thruhulls should be electrically isolated from the hull. You should check this with a reliable ohmmeter while out of the water, or, if in the water, by shorting each shaft or thruhull to the hull and verifying that the Capac meter moves each time. You can use a piece of wire with a sharp probe at each end, be sure to get through any corrosion and down to metal when checking. Please note that the meter movement for a thruhull is pretty small and may be tough to spot in fresh water.
When you say that the engine is isolated completely, I assume that you mean that the drive flange on the transmission is electrically isolated from the shaft. Usually, the engine block itself is grounded to the hull.
The zinc collar on the shaft is there to protect the bronze prop from the stainless shaft. I would definitely install one. Most sources say to put it a short distance ahead of the strut: close enough so that it helps streamline the hub, but far enough that there is a good flow of water to the rubber bearing.
When our boats were built, bronze was the standard material for thru-hulls. They were isolated from the hull to prevent electrolysis with inner and outer gaskets, a washer around the shank, and nonconducting short pipes on the inside. Mine have given no trouble in 35 years.
Still, Marelon is a better material, ABYC approved, and if I ever take mine out, I will put in the reinforced plastic ones, with stainless steel (or marelon) ball valves, if I can find them. Everyone carries Marelon mushroom heads with barbed end, but you cannot use those below the water line. For the engines, a slotted (scoop) strainer end is required, and the valve should screw right to the fitting, with a solid tail that rises above the waterline. You can get the parts from Forespar. The scoop strainer, seacock, and tail pieces all come with straight pipe threads to make a single solid assembly. Do not mix straight and tapered pipe threads!
1975 32' Flybridge Sedan, twin Perkins 6-354 diesels, 1:1.53 velvetdrives, 16 X 19 props. Merritt Island, Florida