Browser makers have declared they’d like to remove them altogether: https://github.com/whatwg/html/issues/2894. But they’re too popular to remove under current policies unless they’re really causing harm, and I do believe there’s serious risk of them classifying it that way. (They’re actually a bit of a maintenance burden, as three of the few remaining synchronous things.)
Remember also the big difference between deprecation and removal. I’d go so far as to say I think it’s likely that alert/prompt/confirm will be deprecated and produce console warnings in at least one major browser before four years pass, though I don’t believe they’ll yet have justified going ahead and removing it.