I'm just getting into shooting. My main problem is finding the time or place to shoot. So when i do its usually about 100 arrows. But i'm no good so take that for what it is.
What i can tell you, is that you can absolutely shoot too much. I am an certified personal trainer and am graduating with me bachelor's degree in exercise science this december. Archery can be thought of like any other sport. If you overtrain, you can get some nasty injuries that will put you out for a very long time. If you are feeling chronic pain every shot that probably means your muscles, tendons and ligaments are damaged and inflamed. You might want to get those checked. You could have burstitis, or some other rotator cuff problam. They need time to heel and reduce swelling. And if not fixed could lead to a full or partial tare in your rotator cuff, or some other injury. This can happen if you do too much in general, too much too soon, or if you just jave poor form (not poor form in accuracy sense but poor form for injury). Just like with a runner who has shin splints or runners knee, you're going to have to take a brake for maybe a month or so. If it's really bad, you might want to talk to a physical therapist. When you are healed, you need to make sure your technique is spot on, and that you take it slow. If you slowly build up over the course of many months of consistant shooting your body might be able to handle shooting everday again. But for the meantime it might be best to start with 2 or 3 times a week. Maybe a a dozen or two a day. Then after each week increse the arrows a day, then maybe add an extra day after a month or two. But listen to your body. Like any workout your body needs time to repair itself. You get stronger in the recovery.
A hiatus won't permenatly damage your accuracy. You might be rusty the next time you pick up the bow. But after a week you should be back to where you were technique wise, but not necesarily strength. Taking days off in your regular training is going to have no consequence either. However, fewer shots a day with a little higher frequency like a dozen arrows 4-5 days a week is better than 3 dozen arrows 2 times a week. But thats concerning technique. Strength wise, 3 dozen arrows 2 times a week is better for buding strength and getting adequit recovery. So it all depends on your goals: building strength so you can shoot frequently, or honeing your technique after you've built that strength.