This will likely follow a similar pattern to email, since it's starting from a very similar position.
At some point people will begin to assign identities to instances and imagine (rightly or wrongly) that being on an instance says something about a person. People do that with cars, shoes, and yes, even email domains.
From a technical perspective, right now Lemmy is as anonymous as can be — I've yet to see an instance that requires ANY kind of verification. I didn't need to provide an email address, phone number, or any other identifying information to sign up. Didn't even need to solve a captcha. I just choose a name and set a password and BOOM! I was in.
Once upon a time, email worked this way, too. Then came the spammers, scammers, and other bad actors, and this was deemed untenable. Nowadays, any email provider that allows anonymous signup is likely to be blocked by most of the email-using world. You won't be able to use them to sign up for other services, and you might not even have your mail accepted by other providers.
This will definitely become a problem as Lemmy becomes popular, and instance admins will need to crack down, lest they be overrun and defederated by the rest of the world.
I'm not sure what the answer is. This is a problem that has not been adequately solved, IMHO. A few bad apples spoil the bunch. That's been true since long before the Internet.