I think (and I may be wrong) that the busses they use while the skyliner is down are repurposed/reallocated busses already in service. Say if busses are normally on a 20 minute rotation, if the skyliner goes down they can reroute however many they need, and push that 20 minute to a 22-25 minute rotation for everyone else until the storms die down.Nothing is perfect but I feel like skyliner issues are more common than monorail or bus issues. But as you said it is probably the best intersection of capacity and cost. I'm just not sure how much it actually saves, because they have to have a fleet of buses and bus drivers at a moment's notice in case it does go down. The more destinations the Skyliner serves, the more backup buses and drivers they need. But I'm sure Disney knows down to the cent. Perhaps the fact that they do know is why the Skyliner hasn't been extended.
They may have some ready on standby, but I doubt it’s the full amount needed - that defeats the entire purpose of the skyliner. But as you said, with more destinations, they require more backups (or in my scenario, they’d reallocate more, making the experience significantly worse for other resort guests)