I'm not familiar with Jon boats, but I'll toss in my general idea of dealing with the wind.
First, when windy I like to go INTO the wind. You can't really do anything to be more precise than that. So a VERY powerful bow mount motor is a good idea. You can always turn it down, but you can't turn it up.
Run directly into the wind with the trolling motor. A strong motor can overcome some serious wave action.
If that doesn't work, I'll turn the boat around and use a kicker motor (or main engine) to go backwards into the wind. This is more precise than going forward into the wind. Usually in this case splash guards on the transom are a good idea because you can take on water when backtrolling in heavy winds.
The other option is to go forward, using the kicker or big motor, and the bow mount to correct the path. This requires an electric steer motor, and a wireless pedal setup could be nice to eliminate the cord, otherwise the M/K brand motors with electric steer have very long cables.
The other way is to setup one or two drift socks, from the transom, and let the wind carry you on a drift. You will be going away from the wind in this case. You will use the bow mount to make path corrections.
This way works when fishing alone and you can get away with one sock off the transom.
When positioning the boat for two or more people you almost need two socks. One attached in front and back to maintain a sideways drift.
IMO if it's really rough, I would look at a tree stand safety strap type of thing to attach to you, or your belt, and go around the fishing pedestal just in case. This is more something I've considered and will probably do for Musky fishing. I can't see doing any other kind of fishing where I'm still out when it's that windy.
A spike anchor or whatever you call them with some rope is a good idea. I use this in case I get blown into shallow water and need to STOP the boat before I get blown into a situation that is going to be VERY hard to get out of. This is for emergencies. You don't need a ton of rope because you will usually drop it once you are already in shallow water.
These are the things I've come up with because of a determination when buying my own boats to never be forced to get off the lake because of wind. Something I had to do growing up fishing with my father and brother.