As others have already stated:
No verbal, somatic, or material components are required to use a spell-like ability, nor does using one require a focus or have an experience point cost.
For completeness:
A spell-like ability has no verbal, somatic, or material component, nor does it require a focus or have an XP cost.
So the spell itself doesn't work right, RAW, or at least not as it was intended to work. The spell never actually says that the gem the target is trapped in is the same gem as the material component (unless I missed it somewhere). So RAW, it requires two gems, one with a certain value (based on target HD) that gets consumed, and another of indeterminate value that their soul and body is trapped in, which could just as easily be a 4 gp hunk of agate. The fact a Molydeus can cast it as an SLA just removes the first one, apparently.
Although RAW the SLA doesn't need the focus component, you can only trigger that version of the spell by having said focus component for the target to pick up. The Focus isn't
required for the SLA, but there is nothing preventing the Molydeus from using one anyway.
Edit: Another interesting quirk - Shades (Sor/Wiz 9) can duplicate any Sor/Wiz Conjuration (summoning) or (creation) spell of 8th level or lower. Trap the Soul is Conjuration (Summoning). Shades (by virtue of inheriting much of itself from Shadow Conjuration) only has verbal and somatic components. The only downside is that the target gets an extra Will save, and if it is successful, then the spell is only 80% likely to function. The spell would either have to create a gem out of shadow-stuff, or you would have to provide one of indeterminate amount.
Edit 2: Pleasure Devils (FC2) also get Trap the Soul as an SLA, as do Ak'chazar Rakshasas (MM3). Shadow Giants (FF) get Shades as an SLA.