I think the pod drives are a great idea. So far as I can see they aren't any more vulnerable than the V-struts, shafts, props and rudders hanging down from our own twin engine boat. If they're engineered properly they should shear away from the underside of the boat without leaving a big hole. We can do it with the turbofan engines on our airplanes, so no reason why it can't be done reliably with a drive hanging down from the bottom of a boat.
As to the drive staying in the water year round, well, so do our V-struts and shafts and props and rudders. What's the difference? You haul out anyway every few years so you scrape the crap off the drives, paint them, and you're good to go for another few years.
The only downside I see to pod drives is the price. Lot of money to move a little cabin cruiser like most people here have forward and backward.
But you never know--- like a lot of high-tech stuff that starts out way expensive, and then catches on and becomes more popular and the cost comes down, pod drives could go the same way. Or not.
I've talked to people who've driven a GB41EU, the pod drive boat, and according to them it's terrific. (GB also has a GB43EU, same boat but with a longer cockpit).
So outside of the current cost, I don't see a downside to them. They make a vessel way more maneuverable even to the point of holding a position desipite current or wind, they can move any direction you like, they allow more user space inside the boat..... sounds like the smart way to go to me if one has the money.
If not there's always the old caveman drive: shafts, cutless bearings, struts, props, rudders, steering wheel, rudder linkages, bow thruster, stern thruster, etc., etc., etc.