I assume those holes were either used in fabrication (to line up for welding or support the parts for painting) or are blanks for a different model/application. You will notice they do not have a reinforcing boss welded on to accept a pin -- they are simply holes punched into the metal sheet. So they do not have an alternate use for mounting a cylinder in this case -- there is not enough meat there to qualify as a mounting point.
Look closely at the engine and rest of the tractor and you will see unused holes and blanks all over the place. Some holes are threaded and have a plastic plug painted over. Heck, even the engine has multiple places for fill caps, dipsticks, etc that are not in use. This type of equipment has lots of variations -- for example the same engine may be used in a tractor, generator, boat, etc, and it's very typical to see lots of extra mounting options. Don't assume they have a purpose in this model/application.
I remember one person here posted about missing bolts on some part of a Kubota just because there were empty threaded holes. Not something to really get concerned about. You'd need a few dozen bolts to fill all the unused holes on my Kubota and there wouldn't be a point.
