Most definitely! YOu have the right idea in that for a slightly ewe necked horse, correct riding techniques will build the upper neck muscles which will counter balance the lower neck muscles that may be overdeveloped. It will also help her to be able to raise the BASE of her neck to get a good arch, from wither to poll.
Have you ever seen a horse skeleton picture? The neck is an "S" shape and it leaves the body rather lower than we imagine; from about the middle of the shoulder blades. It bend forward (the bottom half of the S curve), then goes straightup, then curve the other direction (the top of the neck) and ends at the poll. YOu objective is to raise the WHOLE neck, especially the bottom curve. Meaning , you will flatten out the bottom curve somewhat, which will ift the upper curve and the poll.
The way to do this initially is to encourage the horse to ride with her neck down and reaching outward. The so-called "Long and Low". You ask her to reach outward, but not just let her neck hang off of the wither. She must step forward with impulsions, stepping under with her back legs (stretches the topline) and you have contact with the bit and as she is reaching down and forward, there will optiminally be an arch in her neck. To create this arch, she will suck up the lower part of her neck and extend the upper.
This also helps to relax the lower muscles IF they are overdeveloped.
That kind of overdeveloped lower neck muscles comes from a rider pulling straight back and a horse resisit. Try it yourself. If you pretend that a string is attached to your mouth or better, your forehead, and it is pulled straight back. You don't want to bend your neck so you pull back against it. Feel the muscles on each side of your tracheal go hard and resist? Do that long enough and they will get big and bulgy.
The following horse is reaching forward with a lovely even arch to her neck in what is called the "neck telescoping gesture". Having your horse do this, but perhaps reaching more downward and having a following contact with the mouth is what you are looking for in long and low. neck telescoping example.jpg
Post some pictures some time.