Not all SR ammo is caseless, but yes, Runners tend to use caseless ammo, and EF only works with caseless. The effect on the perception test would be that the propellant is discharged in a different way (namely through an electric charge) and as a result causes less of a bang.
And seriously, don't bring realism into it. >_> Suspension of disbelief shouldn't be cancelled for a simple weapon modification with a small effect, realism lawyers and rule lawyers both shouldn't play RPGs.