Hunter doesn't bond them for a reason. The reason is that they feel (And I agree) it's more important to protect them from stray current by keeping them isolated, then it is to protect them from galvantic corrision, as a stray current can eat away at your thru hulls much much faster, as in weeks, compared to the years of galvantic corrision.
Why? Because if you have 110 volt leak into the ground and the ground is bonded to the engine, then there is going to be so much resistance at where the water meets the zinc, that the rest of the current that can't flow through there is going to flow through your thru hulls. And if the 110 volt isn't grounded at the engine but the thru hulls are still bonded, then that opens up current floating through the water from the stern, up into the shafe, along the bonded wire, and back out into the water via thru hulls taking part of your thru hull with it. Remember, current always takes path of least resistance.
Hunter also doesn't connect it's 110volt ground to the engine for the same reason. It is more important to keep the 110 volt system away from the prop as a short in the boat can eat away the zincs in no time and then the prop when it's coming from the 110 volt. It also exposes your boat's prop to other boat's and dock 110 volt problems. Hunter believes the dock should provide a good ground for the 110 volt system.
The only downside to this is, if the dock doesn't properly ground and neither do any other boats and there is a stray 110 volt current, you are at danger if you touch something that is charged and something grounded. Usually, that would be the shrouds and the dock, like getting off the boat and holding onto the shrouds, however, this is the reason why hunter doesn't bond the mast to the engine either. So even if there is a stray current, you shouldn't ever get stung and sooner or later it's going to find a way to ground safely. Do note that Hunter does bond the mast to the keel bolts to protect the hull from a lighting strike.
Summary, Hunter believes this is the way it's supposed to be and I agree with them. Do not bond your thru hulls to the engine, or the mast to the engine or the 110 volt ground. Just replace your thru hulls once every 10 years...maybe replace them with plastic ones if you are comfortable with them. Less weight, that's for sure.
Hunter has been building boats for a very very long time and they keep improving, or at least trying new things. Some things they have perfected and I believe this is one of them.
It's also a good idea to get one of those spacers (forget the techincal term) that goes between the two cuplings where the shaft meets the transmittion. That will stop all outflow of electricity through the shaft and you will not have to worry about electrolysis destroying your prop as long as you replace your zincs once a year.
Speaking of zincs. Always put two on. The first one is a warning as one will eat through first and fall off. If you only have one after a few months, you have a problem but still have another protecting the prop while you figure out what to do about it.