While Janeway’s AI iteration will be the way fans experience the character when Star Trek: Prodigy first takes place, it’s not completely out of the question to think the actual Captain Janeway might appear in (animated) person at a later point.
The events of Star Trek: Voyager took place from 2371 to 2378, meaning Janeway is still alive during the events of Star Trek: Prodigy five years later.
Of course, it’s not entirely necessary for fans to see her in the series as Janeway, all things considered.