It would be a good idea to check the alignment after a lowering job, but aftermarket caster camber plates will not be needed if you are using stock type springs such as the ebiachs. the 2000 Cobra R came with shorter ebiach springs from the factory and it has stock camber caster plates.
You will be fine lowering your car, it wont alter your alignment very much, if at all. Caster camber plates are a two fold mod... one, you get more adjustment range when alignment is done, this helps for guys (and girls ;-) ) who want more aggressive alignments for the track. Two, if your car is dramatically lowered, the stock c/c plates might not offer the adjustment range to bring the car back to proper alignment values.