Most of the area is in the 30-60 feet above sea level range, so unless you're really close to the bay, flooding generally isn't seen as much of an issue. County surge maps that will give you a general area of trouble spots are here:
http://www.co.okaloosa.fl.us/severe_weather_hurricane_surge_maps.html
(and if anyone else is reading here, check out the Destin West map for an idea of just why it's such a bad idea to buy in the Holiday Isle area)
Also, the geography of Choctawhatchee Bay makes for less of a flooding concern on the north shore-
you've got a 40 mile line that the water can flow against, not a very narrow and skinny funnel like you get in Mobile Bay, Escambia Bay or Tampa Bay.
One thing to look for wherever you end up is underground utilities. Where I live is all underground, and we never lost power during Ivan. The big problems the area has during storms are non-native trees going down (laurel oaks are evil) and moderate roof damage in some areas, and post-Opal roofs are under a newer, much tougher roofing code.