Kroom EMP missiles are very powerful against fighters as usually only one vanilla missile is enough to completely disable them for several seconds, that's why i think it could be useful to have one, smaller than vanilla, to use as a fighter vs fighter weapon.
Vanilla EMP missiles are effective because they fire another missile as soon as the fighter starts to re-power and stun lock it, but kwhwwymwn is talking about shield breaking. Something like this takes 11 full size EMP missiles to get one of the shields down (not all missiles to the same shield because it spins out of control once the cockpit is depowered so performance will vary). With the shield linker powered down before the test it still took 5 EMP missiles to drop one of the shields. It takes 5 missile racks to completely drop the shields hitting where they overlap, or 4 is the linker is shut down.
A less capable EMP missile that was also single shot and thus unable to stun lock does not seem like it would be competitive with the existing fighter missiles. Not giving any regen time will reduce the numbers of missiles a bit, or probably quite a lot in the case of an active linker, but they'll take quite a few to shieldbreak if the guns are struggling and be less versatile.
You can try making it if you want. Underpowered options don't much effect game balance. I just don't think it's going to achieve what you hope and trying to make it do so might negatively effect game balance (eg. removing the HP buffer on phase shields might cause problems on fighters with tight haulage budgets).
