>Because if the CIA went into a courtroom that was open to the public and asked for a warrant that was part of a legitimate investigation into a group planning an attack on the general public, then there is a good chance that the group could find out about it.

You may wish to read the Federal Rules of Criminal Procedure Rule 41 (http://www.law.cornell.edu/rules/frcrmp/rule_41)

You must consider there are reasons that the Rules are drafted in such a way, 1. they are Constitutional protections, 2. they are based on the collective jurisprudence.

I do not believe what is mentioned in the Rule is the existing procedure for filing "under seal" which has been created to take into account everything under the sun that should not be available for public examination: such as terrorist activities, names of minors, child pornography, ect...