Let's take your questions in order.
I do not recognize the maker of the unmarked chairs, but I doubt they are Stickley or Limbert. By the second decade of the 20th century, hundreds of small furniture manufacturers were producing Mission furniture; the style's popularity and simple lines made it easy to produce at a profit. In my area, update New York around Syracuse, there were at least a dozen manufacturers of Mission style furniture. It does not appear that there is much upholstery to save on these chairs, but in any case having them reupholstered will not adversely affect their value.
From your photo, the seats on the six Stickley Brothers Quaint 479 1/2 chairs do not appear to be in poor condition, although you do say that the seat frames and plywood base are beginning to fail. If these were my chairs, I would ask a restorer for advice; I would think the original materials could be repaired and made sound enough to keep in place. I do believe that replacing or reupholstering these seats would reduce the value of these chairs. I have recommended to collectors that if they are intent on new upholstery, they should remove and store the original seats that could be reproduced with your choice of upholstery.
The different catalog number on the chairs you describe as similar to the 479 1/2 models could indicate a different production date, a different type of seat or some small dimensional change that might be undetectable. (I am including part of a page from the Stickley Brothers catalog, showing a 379 1/2 side chair, which is cataloged as a dining chair with an upholstered seat. The 479 1/2 would be cataloged as a loose cushion seat because it can be removed. The 379 1/2 upholstery is fixed directly to the seat frame of the chair.) I would address the seats for these in the same way as the set of six.
Whether changing the original steel glides on the bottom of the legs would affect the value of the chairs may be of little practical significance; if you want to use the chairs and the glides have deteriorated, you don't have much choice. If they are rusted but the metal hasn't substantially deteriorated, you could try simply cleaning them or removing the rust with steel wool and applying a coat of wax to the metal. Glides that have deteriorated need to be replaced to avoid damage to your floors. There are several groups of replacement glides. For chairs that will rest on hardwood floors, I prefer the original steel glides with three-prong attachments; softer materials can become imbedded with grit that will scratch the floors. Chairs that will be used on tile floors should rest on vinyl or nylon glides, which are easily installed with one small nail that is attached to the glide.
Waxing is the simplest way of caring for wood, although there are correct and incorrect ways of applying wax. The two most common mistakes are applying too much, resulting in streaks, and wiping newly applied wax off too soon, before it is dry enough to form a protective surface; the instructions that come with the wax should always be followed. If a piece is very dirty, with layers of dirt buildup, oil-free 0000-gauge woodworkers steel wool is usually the best applicator; if you are simply waxing to create a protective coat, a cotton cloth will work fine.
Lemon oil and other polishes will clean furniture but offer little protection and can be harmful to the wood's finish. Commercial so-called "lemon oil" has little to do with lemons; it is basically lemon-scented kerosene. Spray-on dusting agents may not be directly harmful, but they contain silicone, which can prevent subsequent restoration of an old finish or replacement of an inappropriate finish because it will prevent a new finish from adhering to the wood, even after being stripped.
If you are going to move beyond the care of your furniture into the area of restoration and/or conservation I would recommend some reading. Bruce Johnson has written several very helpful books. One is The Weekend Refinisher, which walks you through different types of restoration for different styles of furniture. Another is The Pegged Join, which deals primarily with Mission furniture.
Although it is out of print, it can still be purchased online from the Craftsman Farms gift shop in Morris Plains, N.J. (stickleymuseumshop.safeshopper.com) and from used-book sellers through Amazon (amazon.com/Pegged-Joint-Restoring-Furniture-Finishes/dp/1886840008)