Disadvantages: Bound to be heavier, more affected by wind, harder to get in and out of under certain situations, and could be harder to fish out of.
Advantages: MIGHT be more "seaworthy......" Maybe.
Freeboard DOES NOT automatically equate to increased safety -it does create the illusion of it in some hulls.
I've got a little Valco U-12 that has a 15" transom and standard utility vee freeboard on the sides. But I've ridden in 14 footers with more freeboard that were a much wetter ride than my boat under calmer conditions than the worst I've had mine out in. Sounds unbelievable, I guess, but there is more to a seaworthy hull than freeboard. Stratigically placed spray rails, sides that flare out so the boat is wider gunwale to gunwale than chine to chine, and things of that nature also play a role. Old Valcos like mine, as well as the similar Gregors of the same cartoppable utility style, are among the driest riding 12' -14' tin boats out there, IMHO, because of the engineering details of things like bottom shape and hullside flare and spray rail placement.
I used to have a 13' Boston Whaler Super Sport.... The Jeep of the marine world, that thing was.... It cured me of automatically assuming that a bigger boat with more freeboard was more seaworthy than my little Whaler by default. They don't have a whole lot of freeboard, but they're one of most seaworthy little boats out there in spite of that. There are a whole host of larger boats with deeper sides that I wouldn't want to cross the 26 miles of Pacific Ocean between Long Beach, CA and Catalina Island, but I had no qualms at all over doing that in my little Whaler. There aren't many boats I'd rather be in when you can stand up straight and tall while in the trough between two swells and not see anything but 7' walls of water on eiher side of you. And I'd rather have an old 13' Whaler as a family boat than most of the "family runabout" style stuff (like the Tahoe line Bass Pro sells) out there.
Preferences are personal, but I prefer to fish from a boat with as little freeboard as possible. YMMV.
T/C