Dear Ann
Ah yes, may the force be with you. But as to your floor, well, that would not have been my choice to darkly stain an already dark wood. And then apply a light colored finish on it. But what's done is done. It's the light colored scratches on the dark background that you find disturbing. To some degree it's just the nature of the wood and the finish you chose. Wenge has a very fine grain also tends to show scratches more, and long expanses of wood with large windows won't help either.
But let's see what your choices are and the consequences of using wax. First, I would follow the contractors suggestion and recoat. Five coats are just about right in a high use area like that anyway. You should have all the deep scratches touched up with two coats first and then the whole floor should be re-coated with a catalyzed water base finish like Street Shoe (Basic Coatings) or Traffic (Bona Kemi), although there are a few more good products out there.
After the recoat, why don't you try to always wear socks or slippers on the floor never outside shoes. Be thorough about putting felt pads on all the furniture, and see if this all prevents future scratches from occurring. This is what I do on my floors, and I plan a recoating every 10 years in low use areas, but kitchens need a recoat every 2-4 years depending on how they are used. The seams of the boards in the kitchen especially need this re-sealing to keep the floor water repellant. Try the Wood Wash cleaner I suggest in the article, it's great stuff, and no they don't pay me to say that.
Now lets talk about waxes. Never, never, never use a solvent based paste wax on this floor. If you paste wax this floor you will not be able to recoat it, and the wax does not provide a durable surface. In the kitchen, the paste wax, (sold in those little tins or in a liquid form described in the second part of that article) will turn white with each water spill. As you can imagine this stuff will cause you no end of grief.
And, I wouldn't in your case use the acrylic polish like Top Gloss that I also mentioned in the article. You have a matte finish on the floor (good choice), and the glossy finish of the acrylic polish will certainly confuse things on your floor. Don't worry now, there is something that I can recommend for your situation. That would be the Bona Kemi Refresh polish. It doesn't have much of a gloss, and it applies easily in either spots or entire areas. But the real advantage of this finish, is that it allows you to recoat the floor later with a water based finish without any adhesion problems.
Both the acrylic polish (Top Gloss) and the paste wax will prevent you from ever recoating the floor in the future. You might be able to remove the acrylic polish, but this will require an ammoniated stripper, it's a lot of trouble. And it's not possible to remove all of a paste wax, to prevent peeling of the next coat of water based finish.
The Bona Kemi refresh kit is what the prefinished floor guys use to disguise scratches when installing these floors. And the company claims it will not interfere with future recoatings. The claim is somewhat believable because Bona has been making water based finishes for about 2 decades. I don't think they would stick their neck out just to sell a few bottles of this stuff. Here is the URL http://www.bonakemi.com/productspecs/refresher.html
You should be able to order this stuff directly from Bona, if you cannot find it locally. Use it sparingly and it will wear off on it's own in about a month. Keeps you coming back for more, eh ? So, do the re-coat with a water based finish for sure. Keep high heels and shoes off the floor, and felt under the chairs. Lift furniture, don't drag it across the floor. You may find that the finish will look better longer with this more gentle treatment. Use Bona's refresher sparingly, and worry less, my princess, about the deep scratches. Just expect to recoat at least the kitchen and high use areas in about 4 years time.
Otherwise, live long and prosper, and may the force of wood floor wisdom be with you forever.