Assalam-o-alaikum!
1. There may or may not be any difference between the two (cracked and licensed), depending upon type of software cracking used. While you can rely and depend upon the analysis / design results in case of a licensed software , but not in case of cracked software (nobody will take responsibility for that), even if there is no difference of results. This is because of the fact that use of cracked software is incorrect ethically as well as legally. You cannot defend or justify use of such software, for the design of real-life structures, in a court of law.
2. CSI has several kind of licenses. I am sure, there will be one fulfilling requirements of your organization, too.
3. See answer to your question 1 above.
Regards.