A couple things come to mind.

The physical activity of looking for poops, bending down to get it, getting up, and putting it where it belongs, is a very monotonous task which requires focus and cognitive power, but is full of tedium. You need to really use your eyes to hone that hand-eye coordination for picking up multiple, small things. I think that cognitive and physical exercise can be migraine inducing. A parallel I’d draw is if your son would get a migraine from needing to weed a lawn?

A big reason this is my initial reaction is I get a major headache from wearing my glasses, which are out dated in prescription, only when they are worn while doing something needing visual acuity. I can wear them for days on end, but if I need to sit in a class or look at my phone excessively for detail oriented work, I get a crazy headache because of the strain.

I think Wick is probably onto something here.

Do the poops have much of an odour?

Generally rabbit poop doesn’t but when the mark territory, there is a substance on them that makes them smell a bit. Maybe your son is sensitive to that? Like a protein allergy?

Could your have a problem with his eyesight? People that need glasses often get headaches, long before they realize that they don’t see very well. (This happened to me). You can get really tense neck- and facial muscles from having to strain to focus your eyes, but you often tense up without knowing it yourself, it gets so automatic. Are the migraines one-sided? Are his neck muscles tense?