Not necessarily. Vixen's powers are rooted in magic, but she was still part of the team versus the Legion of Doom in season 2. I mean, you could just as well say that a tech-based hero like Ray doesn't fit into this season's supernatural focus, but they've managed to make good use of him, both by having him develop tech to fight magic and, more importantly, by focusing on who he is as a person rather than just what he can do. Constantine isn't just a guy who does magic, he's a deeply screwed-up, morally challenged antihero with a ton of personal baggage. There are plenty of ways to get stories out of that regardless of the nature of the threat.
I mean, sure, the most obvious answer to why he becomes a permanent team member in the first place would be to combat a supernatural threat, but there could be some other reason he joins. Maybe he just gets in really deep trouble on 2018 Earth and decides the Waverider could be a good place to hide from his enemies. Or maybe he's hoping he can use time travel to undo his mistake with Astra Logue, to save her soul and his own. Or maybe he figures that if he does enough good deeds as a Legend, he could earn his way out of damnation. (Which was basically his motivation for helping people on the NBC series -- perhaps he decides that helping individuals hasn't done enough to earn redemption, so helping to save the world and all of history could have more impact.)