"This is a really interesting question; I don’t think the rules actually say." I'm quoting KRyan because I said the same thing out loud after reading the question.
On the one hand, it seems like holding the charge might be a whole new "phase" of casting a spell; I'd break the normal flow into three "phases": ready (spell slot form), casting (where magic words are spoken, and as KRyan mentioned, counterspell and interruption are possible), and result (where the effect occurs).
It seems like touch spells have a weird phase 2.5; the spell has been cast, but the effect of the spell itself hasn't occurred.
It probably shouldn't be considered a "spell effect".
Holding the charge is something you do with spell energy from a touch attack. It's not a part of the spell itself, but rather a feature of spell-casting as a whole.
On the other hand, there doesn't seem to be an official definition for "spell effect".
Because of this, I'd be inclined to rule that spell effect simply means "any magic stuff that's the result of a spell". In this case, even though "the charge" isn't a listed effect of a spell, it's still part of the result. I would consider it equivalent to the "glowing, pea-sized bead" that embodies a not-yet-exploded fireball.
Because a held charge is absolutely a magical "effect", and it's specific to a particular creature, I would treat it as a spell effect. However, the ability text states that "[a] spellthief can steal the effect of a spell only if the spell could be cast on him by the original caster." It then goes to explain how the shield spell cannot be stolen because it is cast at a range of personal. With that in mind, because the original caster could not have given you the charge in the first place, you cannot steal it. That is, while you can steal the effect of a touch spell (the bonus from Bull's Strength, etc.), you cannot steal the held charge itself.
With that in mind, I'd say you can suppress the held charge on the target (from the description):
If a spellthief tries to steal the effect of a spell not allowed to
him, the effect is still suppressed on the original target of the
spell for 1 minute per spellthief class level.