Back atcha again! Actually I tried to answer this question earlier over on KFS, but it got deleted before I could send it. But you have sort of answered your own question. Anything, such as heavy California kelp, heavy Florida spring-fed stream vegetation, trot lines, boulders, etc. can and will foul the Mirage drive. That is one reason why Hobie, in its wisdom, provided a bungee and a hook for hooking one pedal back. This folds both flippers or sails up against the hull. Thus you have only about 3 inches of the Mirage drive exending down beneath the keel. Then when you get into such conditions, or expect to, just hook the bungee on to the pedal shaft and this flattens the flippers up against the hull. Or, even better some times, just pull the whole drive and lay the flippers up on the bow. Takes no more than 10 seconds to do. Of course, you should always use a leash/lanyard/line to secure the drive to a cleat or eyestrap in the cockpit, whether the drive is in place in the well or free on deck.
So to finally answer your question, the Hobies are both ocean and freshwater boats. You would not knowingly steer a paddle-only yak over a shallow boulder in a stream any more than you would a pedal boat. Hobie also supplies a plastic plug that fits the Mirage drive well when the drive is out, in case someone does not like being that close to the environment.
But I have rarely used mine since it is just one more thing to remember to take, and find space for.
Here is a pic of the cockpit of my (wife's) Sport showing how I rigged the leash. Note the large bungee hook on the port side of the Sport, and the leash attached to a SS shackle right on the Mirage drive. This pic also shows my home-made tackle box bungee that used to come as standard equipment on the earlier Outbacks before the 8 inch hatch came as standard equipment in front of the seating area.