Unfortunately, there are very few EX250-specific hard luggage options available. Most of them require making your own parts. Below are a few examples of homebrew hard luggage systems.
Example 1: Ventura Rack + JC Whitney/Givi topcase.
You can acquire a ready-made Ventura rack and install a JC Whitney or Givi trunk. This system is very simple to install, and there is no need to make your own parts. Picture taken from Troy's profile.
Example 3: Two Givi Hard sidecases permanently mounted to the bike. Courtesy of quixotic
Quixotic manufactured a rectangular sub-frame out of aluminum square stock and bolted the boxes to it. Detailed instructions can be found here.
Example 4: Homemade rack + three Givi Hard cases
This setup features a DIY rack. Courtesy of viajero (no profile)
Details: 3/4" copper pipe (type L, thick wall) with 3/4" wood dowel running the length of the pipe and as far into the elbows as possible. This should add a lot of strength and crush resistance. Joints are glued with JB Weld. There are two copper rivets in each joint for added strength. All holes have a dab of silicone as well to seal the pipe. Because of the wood inside, it is advisable to waterproof the joints. A particular challenge was drilling the mounting holes to match the angle of the holes for those bungee hooks. Those holes are also filled with silicone at the final mounting.
The rack sits high enough to be able to lift the seat, slide it back and then lift the front and remove. The boxes are mounted just far enough forward and do not interfere with the turn signals.
Example 5: Another homemade rack + three Givi Hard cases
This setup uses passenger footpegs and the grab bar as rack mount points.
An inexpensive hard bags setup
A set of GIVI side cases for most bikes runs about $800. This is not an alternative that fits within the usual EX250 budget. JC Whitney carries universal mount top cases. Top cases are the cases that sit behind the passenger, either with a bracket or attached to a luggage rack. What was really wanted were side cases (like hard saddlebags) figuring that one could store more in two medium-sized side cases than one large top case.
Measure the space you have to work with before you buy your cases. These are the 'medium' ones, but sizes can change depending on the supplier.
The two cases were about $150 and came with free "universal brackets" to clamp them onto any luggage rack. That's a really cool feature, except that a rear luggage rack is an aftermarket option for the Ninja, and there isn't one hanging down each side, either.
What you do have, however, are 4 little hooks that flip up for the attachment of bungee cords. Bungee cords are of limited use, but the hooks at least make some decent mounting points for what you are going to build. These hooks are held in place by a single bolt, which goes straight through the frame, making it a very secure and sturdy place to attach something heavy. You can't just bolt the mounting plate straight on, though, since the screw is pretty deeply set inside the fairing. You need to extend it out somehow, as well as make sure the cases will still be high enough to clear the exhausts.
Our solution here is to take a solid steel bar, cut it up into four pieces, and drill a hole through the middle, where you can insert a bolt. Other alternatives to the solid steel bar are discussed at the bottom of this page.
The first part is easy. It's the drilling through 7 inches of solid steel that's the hard part. Weapons of choice, after some experimentation, are cobalt drill bits (which last about 3 inches of steel each). This will give you, after a lot of drilling, some steel rods to use as spacers. You will also need to get some long bolts to go through them and into the frame. The hooks were left on, since hooks might always be useful, and they do a good job of holding the steel spacers a bit more securely.
This holds the bracket firmly at the top and works great. Here is the side view:
Of course, the brackets are angled out a bit to the sides to clear the fairing, so they'll need some support on the bottom. The initial solution for this was to simply have a metal rod go through the bike above the tire, holding the two brackets together. This worked great, but on very large bumps, and when riding 2-up, the suspension actually dipped low enough for the tire to hit the bar. It wasn't noticeable while riding, nor was it duplicable in the garage, even with a couple people pulling down on the rear, but tire marks could be noticed on the steel bar after a ride.
So, rather than having the bar go all the way through, the brackets are mounted straight to the undertail/fender. The fender is cheap, soft plastic, so trying to get anything to mount to it is not a great idea. You'll need 4 small rectangles of metal, the kind found in the roofing section of your builders' supply. Cut them down to the shape of the fender, then bolt them to each side of the plastic, sandwiching the flimsy plastic between the two bits of metal. Face the bolts outward to avoid catching the tire on the sharp side.
To connect the bracket to the fender, cut a metal pipe or conduit to the right size and grind down the ends to match the proper angle. Then, glue a wooden dowel inside each conduit piece. Use something like polyurethane glue (the kind that foams up and expands before becoming rock hard). Then drill a hole in each side and use a wood screw to screw from the bracket into the tube. After that, do the same thing from the other side, screwing from inside the fender, through the steel plates, and into the tube. Install that between the steel plates and the bracket for the case.
The brackets are now very secure, and you can easily put pretty much anything in the side cases. They'll each fit a full face helmet, a few 2-liter bottles of soda, or a couple of gallon milk jugs. The larger size would hold even more, but that isn't possible because they'd melt on the exhaust.
Total cost was around $165 for everything.
Alternatives to the threaded rod
Since this is a DIY project, you're going to have to make some decisions for yourself. Here are a few ideas about how to anchor your brackets; poke around the fasteners section of your favorite hardware store(s). You'll find something you can work with.
A word of caution
The tabs for the bungee hooks are welded, pretty wimpily, onto the frame. You really want to reinforce that area before venturing far from home. Your local welding shop should be able to do this relatively easily. Just pull the bags, fender, tail fairing, tail lights, turn signals, etc... off the back of the bike and have them throw on a 3/16" steel plate or something to reinforce that. Shoot it with black rust paint to make it match.