With an isolation transformer in place, in theory, the shorepower ground should go to a faraday shield on the isolation transformer so a really high voltage spike on the shore power side should short to the faraday ground (shorepower ground) which should trip the shorepower circuit w/o affecting anything on the boat.
Conversely, some boats have galvanic isolators rather than more expensive isolation transformers. A galvanic isolator will make it such that a small (AC source from the marina) current will flow to AC ground unless over a certain threshold. The galvanic isolatiors typcially have two .7V diodes so often the threshold is 1.4V. Therefore anything over that threshold would then bleed through and the boat will have AC current passing through the ground system. If this is tied into the DC system, then there will be AC current flowing on the DC ground. Thus, a boat with galvanic isolator probably shouldn't have the two grounds tied together whereas one with an isolation transformer should be able to handle it. With the galvanic isolator, if the AC and DC grounds are tied together, one path of the current leaked across the 1.4V diodes can go through the water--creating a hazard in the water.
If you have a piece of AC equipment on the boat that is improperly wired, and both AC/DC grounds are tied together, then there is a potential hazard having nothing to do with isolation from the shore power. However, there is a much lower chance that the AC current from the defective equipment will leak into the water because there is unlikely to be a second path to the water outside the boat. Well, unless you've got multiple bonded thru-hulls, zincs and so forth...
A good source in the USA of inexpensive marine isolation transformers is Bridgeport Magnetics
. They don't typically sell to the end user (thus, their good pricing I suppose) so you need to know what you want when ordering from them and be willing to wait 3 to 6 weeks for delivery via a freight service. We purchased one last fall to replace an older Triplite isolation transformer and are pleased with the quality of the new Bridgeport Magnetics one. They use a toroidal transformer. By design toroidal transformers are quite a bit lighter than a traditionally stacked transformer. So, instead of having 80-100lb's hanging on the bulkhead, we've got a smaller 50lb box. Nice.