In singleplayer, yes.
In multiplayer, no.
Why? I don't know.
Here's the "Proximity of Detonation" chart
Add ECM shift to 1d6
Roll: Effect on warhead
1: None (does full damage)
2: None
3: None
4: None
5: None
6: None
7-8: Half damage
9: Quarter damage
As you can see, this is not a good way to defend against seekers. More speed would be a better idea. Starbases might as well give it a try, since they can't move.