Well, yes, but I was thinking of something a bit more recent. A forty-year-old example of a Ghost really shouldn't be enough to devise a preprogrammed ECM mode capable of completely disabling the latest models (unless, of course, somebody went and made Microsoft the UN Spacy's prime software contractor).
Of course, the Vajra could be simply using sheer brute-force white noise on the command frequencies, but if they have that kind of power output then why aren't they simply blanking out the sensors and comms on all the Valkyries too? Take away their missiles and computer-controlled gunsights, and those VF-171s suddenly aren't even worth stopping to deal with - just ignore them and blow past toward the capital ships. SMS's VF-25s would be more of a threat, but even their effectiveness would be reduced, and saturating the fleet's inner defences would be much easier than it actually turned out.