I’ve been thinking about this too. Only been on Lemmy a few days, so still only have this one account, but definitely considering creating others, for the same reason as I had different accounts on Reddit: to compartmentalize different interests and purposes. For instance, a technology account, a news/politics account, an NSFW account. The cool thing about the Fediverse is that you can also create those accounts on instances that match the purpose of the account, like tech on programming.dev, NSFW on lemmynsfw.com, etc.
Edit: I just realized now upon re-reading your question that it was specific to Lemmy vs. Mastodon. In that case, I would say definitely. I think the two systems are sufficiently different to warrant having separate accounts. I do have another Mastodon account. One on each system for now.