When it comes to ZSS I think it'd just come down to how they prioritize her. In how Metroid itself would be handled I'd imagine she'd be behind Samus and Ridley, they're more prominent characters and now that Ridley has a working template for the team he probably doesn't have to worry about his biggest barrier to inclusion keeping him out. Dark Samus is more prominent as a major villain in the Prime subseries, but she's also a clone and as we've seen historically, they usually tend to be low priority, and with ZSS I don't think it would be any different.
In terms of the rest of the cast it's more up for debate. Sure, she wouldn't be prioritized over say, the core Mario cast, but she is still a character with a history in Smash and is a liked moveset and that is a reason the team could consider trying to keep her similar to the aforementioned Sheik. So, she may be prioritized over other characters, and if enough time remains, she stays on the roster.
Of course, this is hypothetical as I don't know how the Smash team would truly approach the situation, but I don't think she'd immediately be cut outright. She just may depend on how much time they have and what they can do with it.