Imoen's Belt has only one purpose: to keep players from killing her before you get out Irenicus's dungeon. It doesn't really have anything to do with Irenicus. If you killed Imoen (or if she got killed by a monster), it would look pretty weird when you saw her fight Irenicus and get abducted by the Cowled Wizards in Waukeen's Promenade. It's all about preserving game continuity
Imoen is also protected in other ways in Chapter One. For example, if she reaches 1 hit point, she will run away and meet you in Waukeen's Promenade. Even if you remove her belt and cast Disintegrate on her, she will still show up in the cut-scene when you leave Irenicus's dungeon. The game designers don't want anything to mess up the plot.
The reason why she isn't wearing the belt when you meet her in Spellhold is because the "Imoen" you meet in Irenicus's dungeon and the "Imoen" you meet in Spellhold are actually two different characters. They have different CRE files, different soundsets, different amounts of experience, different levels, different spells, etc. This is also true of other NPCs that you meet in different places. For example, the "Bodhi" you meet in Chapter Three will drain two levels per hit, while the "Bodhi" you meet in Chapter Six will drain five levels per hit. There are seven or eight different versions of Jon Irenicus. This is all perfectly normal and nothing to worry about.
