Hope you both are staying safe down there. Im in Apollo beach and we are just getting some wind gusts and rain.It will certainly have some effect. The big reef will likely have some mild impact. The bigger damage, IMHO, will be the shallow patch reefs that we snorkel. Big waves and big tides in areas around shallow water near small islands will move stuff around.
We were just there a few weeks ago and things were looking pretty good in terms of the recovery from Irma 5 years ago. That was as bad as it could get in the Middle Keys (which is where we like to snorkel). Hurricane Ian will shake things up a bit, but I doubt it will have any big, long term effects.
BTW, below is the noon forecast for Ian. Our house is just above the gap between the '7' and the '9'. Ian will pass by less than 20 mile off shore. Wind gusts here are expected to be over 115mph, but the storm surge, far less predictable, is our biggest concern.
Im staying at a resort in duck key starting October 9th. Hoping to go snorkeling to all the places you recommended to me. Hopefully i can see lots of wildlife and collect some cool stuff