Well, Electronic Warfare as we know it is divided into three subcategories: Electronic Attack, Electronic Support, and Electronic Protection.
EA is essentially the use of EM energy to cause harm to the enemy's ability to make war or do damage. In Freespace, this comes in the form of the countermeasures you use against missiles, and in BP, the jamming of GTVA beam weapons and UEF torpedoes. Terran and Vasudan communication frequencies are fairly easy to detect and exploit, but on the Shivan end, their equipment and technology is on a completely different level. Maybe after the recovery of ETAK and additional research into Shivan technology, the GTVA will be able to analyze Shivan technology and find a way to attack their electronic systems and affect their weapons like the UEF and GTVA do with each other.
The GTVA has been using Electronic Support against its enemies for a long time; basically, ES involves intercepting communications and other signals emitted by enemy ships. Tracking ships through subspace and intercepting enemy comms is the way the GTVA mostly uses ES. They can already track Shivan vessels through subspace, from what we know, and can probably detect Shivan communications, though they probably have no idea what they mean. Again, more research into ETAK might enhance this.
Electronic Protection is making allied units less vulnerable to enemy electronic warfare or countermeasures--such as improving missiles to make them less susceptible to countermeasures and controlling electronic emissions from allied ships (best manifested in stealth technology). Improving EP for the GTVA would probably require a greater understanding of Shivan technology, but with stealth ships, they're already making some great strides.