Solar panels can be protected while in use, however, the entire system must be protected or it will not do any good.
To protect the panels you will need to increase the number enough to compensate for losses, and having a back up set with back ups of the other components in a separate Faraday cage will be a very good idea.
If you want to operate and still be protected you have to start from the ground up. Lay down 20 opi (Openings per inch) or tighter copper mesh on the ground. Drive ground rods and connect at each corner. This ‘floor’ should be large enough, plus one foot on each side, to hold a building that will contain the batteries and electronics for the solar system, plus anything else you want protected that is part of the electrical system.
Stub up metal conduit in a couple of places and run it out four feet or so from the site, securely connecting it to the grounded mesh. Build a wooden structure on the mesh that will contain the solar system components except for the panels. Install the solar panels on the roof. Make standoffs that will be six inches to a foot above the solar panels. Be sure to seal the roof if they penetrate it.
Install one or more metal conduits through the roof and seal them against moisture. Run the solar panel wiring through these into the power house and secure them into place.
Add 1×2 or similar to make a grid over the solar panels. Add a layer of the 20 opi copper mesh over these supports and down the sides of the building. Lace it into the mesh on the ground, making sure there are no gaps. For the doors, cut out the areas for the doors, allowing at least three inches past the door frame. Wrap this around magnetic strips and fasten them to the wall all the way around.
Make panels of the copper mesh to overlap the door and door frame. Add strip magnets to the edges of the mesh and fold the mesh over and secure it so the magnetic strips on the door panel mesh will pull the mesh of the door tightly against the mesh on the wall.
Add two inch risers on top of the first layer of copper mesh and make the wooden grid being very careful not to disturb the mesh already secured. (It will probably be best if this is done at the same time as the first layer to avoid problems.) Offset a second layer of 20opi copper mesh from the first one over the new support grid. Do not let this mesh contact the first layer on the roof. Use standoffs that do not go through the first layer to hold the second apart and drape it over the edges of the roof. About three to four feet down this second layer can be laced into the first layer.
However much square feet of coverage there is of the mesh plus the support grid over the panels will need to be added in additional panels.
Inside the power house, the inverters can be wired up to power lines run from the house. Use a solid copper panel at the point the conduit comes through the mesh. Make a copper box over the conduit end and install gas gap protectors for each power line leg, and ground. This will prevent EMP from coming in from outside on the power lines. Everything else is inside the Faraday cage that is the power house.
To protect anything past that point will require running the power lines in grounded metal conduit, all the way up to the distribution box, which should be metal and grounded. Then, from that box, everything must be in conduit to each appliance. Whether or not these will survive is going to depend on how they might be protected.
If they have much wiring, it could carry the EMP out toward the power house, but the protection where the wires go through the mesh and solid copper panel should stop it.
This is a huge amount of work and money to only possibly being able to run anything on the power that you will have that is not inside the power house.
So says the Devil’s Advocate.