If now Service Desk 3 is separated from Jira, does it mean I will have to (partially) duplicate users/groups in both systems when I want to integrate them?

[Miroslav Hornik]

guys I am unable to thank and answer the answer below because of the point limit, pretty ridiculous and getting some "user not permited" error...anyways...I hope this will work:

Thanks for the quick reply - that's good news. However I was more than confused by the wording used here:

https://confluence.atlassian.com/servicedesk/jira-service-desk-3-0-0-release-notes-770801761.html

for example: JIRA Service Desk is no longer an add-on for JIRA!

[Nic Brough -Adaptavist-]

It's not separated from JIRA - you have to have JIRA running in order to run Service Desk.  Service Desk is an application for JIRA and runs on JIRA Core. 

So, no, your user directories are still provided by JIRA Core underneath it all.