The game is designed for the player to have 3 Hooks at any given time to inspire them into looking for trouble. A Hook taken from a Modification would replace another Hook if you took them Modification. This represents that the Modification seriously affects the character while they're getting used to their new body. But it's not permanent! As early as the end of the Episode, a player may change or refresh their Hooks to focus on what's interesting to them.
Just like in a TV show where a character's challenges and flaws will swap in and out of focus between episodes, a player may have a roster of Hooks they change per episode depending on which locations, groups, & themes are the focus.
Since 3 Hooks per player is a lot for the SM to keep track of, the game is designed to encourage a player to seek out opportunities to apply their Hooks, or a Hook of another player they're curious about.
This is just the default position of the game, a starting point! If this standard style of play doesn't suit your group, the Drifting chapter discusses how groups may modify aspects of the game to suit their specific needs!