For the most part that won't be the case. They'll all be interconnected. Beehaw is the only instance that I'm aware of that defederates as aggressively as they do. If you go to the bottom of any instance and click the "instances" link you can see who they have defederated. Most of them will have none or maybe a few defederated at most. Check out beehaw's and you'll see what I mean.

For a long time beehaw's aggressive defederation and moderation policies made a large impact on the feel of Lemmy as a whole since they made up a decent portion of the user base, but now that there is more migration elsewhere like lemmy.world it's just not as relevant what they do anymore. And with their sign ups being the way they are they will only become more and more irrelevant to the overall feeling of Lemmy. Which isn't a bad thing for them necessarily. If they only want a small safe space or whatever then they are more than welcome to cultivate that however they want. But I wouldn't be concerned about defederation on a larger scale where you never know if you're posting on a defederated instance or not. Like 99% of the time everything will be federated.