Dig the article, and it's obvious what EMPs do, but the movie doesn't sell the concept.
Computers being the heart of cars (much less motorcycles) rather than just functioning as less major assistance is a relatively new thing by my understanding and hasn't completely phased in, so it seems like a niche tactic. It would only be effective on newer cars, so that's a pretty big gamble - especially if you have to stop mid-chase to fire it.
After studying the scene, every car he passes appears to still be driving just fine despite the lights going out briefly, so that makes one think the gun has a pretty soft effect on vehicles, or that the engines of the vehicles aren't susceptible to it (including, obviously, the motorcycle which he fires directly at). The primary focus seemed to be cutting the lights (which were definitely electronic).
Either way, if shutting down the engines was
the goal, it clearly didn't work. Maybe we're meant to assume that Batman guessed his average looking motorcycle might be more cutting edge than it really was.
Which is fine, but the fact that it's so vaguely presented creates a pause in many viewers. One of many 'huh?' moments where the suspension of disbelief is broken by logic gaps or lack of explanation.
Ultimately, the fact that it had zero effect on any engine in the entire scene makes me want to say he was more likely going after the tablet making the transfer.
(And don't get me wrong, I love the concept, and it's probably the coolest 'this is the awesome mysterious Batman you know and love' scene in the whole film - a theme Nolan has lapses in holding consistent. So kudos for what was done well.)