The description of the 3rd-level Sor/Wiz spell siphon [trans] (Complete Scoundrel 103) makes no mention of any restrictions on what spells it can replace due to the source of the siphon spell's casting. That is, the spell doesn't seem to care if it were cast as a prepared spell or if it were cast without preparation. Instead, the description says that the siphon spell effect can replace only expended arcane prepared spells (like those of a wizard) and expended arcane spell slots of a caster that casts spells without preparation (like those of a bard or sorcerer).
Further, with the spell's description including tightly knit language that accommodates casters whose spells are both prepared and not prepared, it seems reasonable to allow a multiclass caster who's capable of both kinds of casting to pick to allocate the spell's effect appropriately however she wants. For example, I'd have no problem in my campaign allowing a sorcerer/wizard to cast the spell siphon and use appropriately the effect to replace expended prepared spells, expended spell slots, or both in some combination.
Were the spell to check the caster's magic style—with or without preparation—, activating a wand of siphon would be complicated as the spell's effect would then possibly be contingent upon the creator of the wand of siphon instead of the effect being contingent upon the spell itself. Under such a reading, a typical wand of siphon would default to creation by a wizard—as that would give it the lowest caster level—, so a sorcerer could still activate such a wand but receive no benefit. That'd be weird and would perhaps make the siphon spell unique among 3.5's official spells.