My sourdough has these holes after overnight proofing. I think they are the result of low gluten development but I'm not sure.
I've used this recipe: https://www.sourdoughandolives.com/recipe/easy-sourdough-rye-bread-recipe/
The first couple of times I tried it I used white rye and strong white bread and the results were actually quite good (beginner's luck?). For this latest attempt I used wholemeal rye (which is what the recipe actually calls for, but mine only has 6.8% protein) and strong white bread flour. I decreased the water content slightly because my recent experiments with wholemeal flours have resulted in very tacky breads. I also introduced a knead at the beginning.
These doughs, as well as looking pock-marked, didn't rise very much. I am totally new to this sourdough baking. I know I should try with easy flours first but I love rye and the first attempts were encouraging.
Rye has weak gluten, if any at all, as you already noticed yourself. Plus it contains something called pentosans, which form a gel when hydrated and are responsible for the stickiness of rye doughs.
So these holes are certainly a result of the high rye percentage and they show there is certainly a lot of fermentation going on. Don't get discouraged because your dough didn't rise much, the gluten network just isn't strong enough to support a lot of gas.
Your dough looks overfermented.
Actually, despite being small and a bit cracked, it tastes very good. And didn't look too ugly, though was slightly tacky
How do I prevent over-fermentation? Shorter bulk rise/proofs?
Yes, I think in your case shorter fermentation is definitely called for.