[Snake]

Kensei/Hexer is better than Kensei/Spellthief. He'd not get as much dodge/Evasion chance as he's supposed to. And he won't be able to get a free pass out of Silence/Interference either due to no Negotiate.

It's not in terms of damage, it's in terms of utility, and some of this 'utility' turns around and becomes damage.

As a Spellthief, Joker has (or could have, in some cases) a team-wide percentage heal (Malmelo)
a lightning augment buff that can be used on the team and themselves (Redgull)
a lightning damage amplifier for 1M, that makes Mechanations automatically weak to Lightning (Splash)
all of Rogue's evasion/hit benefits from the winds
more evasion for several rounds (Distortion)
guess what? more evasion (Fortune Wind)
a way to fucktouple their hit once again and on top of their already 60 scaled SKI/LUC (Invisible Weapon)
a way to blind a single enemy (Pocket Sand)
a way to do an extra 150% damage to feared enemies, and gain +10 to all stats on top of it (Death Knighting)
two to three ways to recover FP (Energy Laundering/Blue Steal/Kensei's passive FP regen)
a way to make a single enemy fuck their own team up if they use big AoEs (Confusion)
a way to remove two/three negative status effects [INCLUDING THE IMPORTANT SILENCE] for just hitting the enemy with Bloody Palms (Negotiate)
and interference itself (Ryemei/Quetal/Black Spark)

Conduiz also helps the part the magical hits will always use your SWA for the lightning spells.

Hexer doesn't offer as much options like Spellthief, if any at all. A Hexer's also always stopped by a silence most of the time, and null shell. AND the most importantly, Hexer can be hit if you build to hit, unlike Spellthieves who can just chain-cast Distortion + Southern Wind + Eastern Wind + Fortune Wind.

PS: The biggest issue is in bold, imo.