I use rapid fire seekers as anti-torpedo counter measures.
Haven noticed any downside from the jitter, but I haven't test extensively with targeting external modules.
When testing in the 2.1 beta jitter affected the missiles,
they were simply not launched straight, but that has no effect
on weapons that home in on target.
Specifically when using packhounds you see the added jitter,
as they launch using the jitter mechanic to spread,
and then home in.
So OP, no seekers are not affected and on the effective engagement
range of dumbfires you won't notice much either.