On average, in the long run, both approaches are the same, since it’s the same roll one way or the other.
Rolling just once per spell will result in a swingier result: you are closer to an all-or-none situation rather than possibly getting some but not all. It’s also faster in play, particularly when there are a lot of targets.
But if you roll enough times with either method, eventually your results will tend towards the same average. Rolling more (per creature) will tend towards that average more strongly.
Anyway, the official rule is
If your spell is being resisted by a creature with spell resistance, you must make a caster level check (1d20 + caster level) at least equal to the creature’s spell resistance for the spell to affect that creature.
This very much describes a pair-wise situation: a creature resisting a spell. You are rolling a check against that creature’s SR. If there is another creature also resisting that spell? Roll a separate check against their SR. (Note that Pathfinder uses absolutely identical language for this.)
As a result, rolling just once per spell is a houserule, probably intended to speed up gameplay.