It's difficult to tell without seeing how you hold the guitar in person or even knowing what kind of guitar it is. If you have to hunch over then yes you will get upper back and shoulder issues. Have you tried using a strap to raise the guitar to a comfortable height? You can use straps while sitting down if you don't have it stupidly low. Otherwise the only alternative is to raise your knee and you said you didn't like a foot stool so...

One question would be, at what kind of angle does the guitar sit relative to your body? Does the back of the guitar sit flat against your stomach or is it at an angle with the headstock angled away from you? If the neck is too far back towards you it puts extra stress on your shoulder as it is in an unnatural position which is why most real guitarists have the guitar pointed out at a 45 degree angle and resting on their ribs. That way the range of movement for your shoulder, elbow and wrist are all much more comfortable and easy so you can play better for longer and not get fatigued or injured.