Welcome to the dark side--kayak fishing--and especially to the world of the Hobie Mirage Drive. In answer to your questions, here's my take based on personal experience over the past 3-4 years with both the OB and Sport.
1. A Hobie Mirage Drive yak would be no more a bad choice than any other yak. Is your dealer a Hobie dealer? If so, then he needs to get out more with his boats! If you encounter "rocks, stumps, and shallows," simply fold the fins up against the hull and secure the pedals with the included bungee hook. If this is not sufficient, simply pull the drive (takes all of 10 seconds) and place it on the bow attached by a leash, line, paracord, dog leash or whatever--no big ting. Easy to reinstall, if and when you wish--might take 15 seconds since you sometimes have to rock the drive a bit to get it settled in the well.
2. Or you can leave the drive in your truck or at home and just use the paddle, if you think you will running rapids or getting into heavy stuff continually (which is very unlikely). The paddle does work as advertised, but few of us use it for fishing (or much of anything else, except maybe backing down), since the hands-free part is great. Just an occasional tweak with the rudder is all most anyone needs when drifting down a river, or in the open ocean. Hobie even has a plug that fits into the drive well, if you will not be using the drive, but I have rarely ever used mineâ€”no problemo.
3. Common sense is your best friend when deciding how and where to use the drive. I rarely remove mine except when in heavy freshwater vegetation such as lily pads, or in shallow water over oyster reefs or rocks with a strong tidal current running (~2 knots or so). You will NOT tear up a Mirage Drive unless you are not paying attention and do something especially dumb, and even then it would have to be REALLY dumb! Lots of folks, including Hobie staff and sales people do not even remove the drive when pulling a boat up on the beach during a demo day with rarely a problem. The Mirage Drive is a precision piece of equipment, but tough, just like a fine fishing reel, so treat them both with respect and you should be OK. Just my $.02.
Hereâ€™s my Sport pulled up on a Forgotten Coast oyster bar with the Drive fins folded up against the hull.