imo it doesn't matter for Lemmy right now one way or another, and maybe not ever. Being federated with Threads doesn't do anything yet. Defederate or not, the only change (from my understanding) is about making a statement, or standing with other microblog platform instances that made a choice.
On mastodon however, I'll likely either use a federated instance or run two accounts. It's very likely that some person I want to follow will be on Threads, and until people can convince them otherwise ¯\(ツ)/¯
What's nice though is that if Threads is on activitypub, you won't need to log in to see the content. It's only if you want to engage with the content, and that can be done from a second Mastodon account.