I wouldn't trust it, personally, but it probably depends on exactly where the holes are, how deep they are, and what other damage it might have sustained in the fall.
Some helmet manufacturers will inspect helmets for free (moto helmets anyway, and I assume bici helmet manufacturers do the same) - of course that means sending it away, but if it's an expensive helmet you really like, you could buy a cheap one for the interim.
But ... how many marks, and are they on both sides? Is it possible they're the holes where a visor is supposed to pop in? My helmet has those even though it didn't come with a visor - I suppose that means Specialized sells the exact same liner in "road" and "MTB" trim.
Speed comes from what you put behind you. - Judi Ketteler