Roman Pearce: Why are they shooting at me?
Tej Parker: I don't know. Maybe because you're in a orange Lamborghini.
Roman Pearce: Shut up, Tej.
Using an EMP to disable the security at the base would render anything electrical useless, computers, cars, cameras, anything with a micro chip in it. Firing a EMP directly under something you want to steal like a submarine is completely stupid - Cypher would know this.