well..the fact is.. EMP missiles actually do insignificant damage to capital shields (if any)..also you need 100 missiles to drop ordinary transport shields (providing that they actuality work...but from what i saw they don't)...
however...they do work on fighters...and they work great...
for capital ship sheilds guns are much better answer...cheaper, no chance of dropping your own shield, and guns are probably more precise...u can't simply miss big ship with guns...:P