Well, that was a poor test.
Vaygr large capital ships are immune to EMP... Or very nearly close to it.
Well, I finally was able to disable a large capital ship... But I had to crank the disable effect "up to 11"... And it sat disabled until it was destroyed.
I turned the disable effect down (only slightly), and learned something interesting. Given no other targets, the EMP corvettes will keep a disabled ship disabled, but not by continuously firing. There's an internal game mechanic at play here, but basically they keep track of the disable repair rate, and once it hits a certain value (probably based on the amount of disable of the weapon), they'll fire again, dropping that value back down to (or near) 0.