We hope not! But as we've seen, Nintendo isn't averse to removing even its big-name Super Mario Battle Royale from the service, so we certainly wouldn't get too attached to this one.
If there's a sliver of hope that this won't be retired after a year or two, it's that F-Zero 99 was an internally developed, cross-company project with Nintendo Software Technology heading up development (as evidenced in the credits, which you can watch at any time from the Options menu). Conversely, development on all the previous entries in this loose series was primarily handled by external company Arika.
Whether the fact it was developed internally makes any difference, only Nintendo can say. You might argue that Tetris 99's continued survival is down to its function as a marketing tool which periodically hosts tie-in events to new releases. F-Zero doesn't have that brand of cross-promotional potential, perhaps, but let's all cross our fingers that Nintendo sees fit to keep this one alive for a long time to come.