Smart-QL won't give you an access to data you cannot see in JIRA. Jira permissions, roles, groups are supported by Smart-QL. Smart-QL queries will behave just like JQL queries and simple Jira searches - they will return only data user can access to see.
This means that if your Jira contains hundreds of issues but on of your users - John - can access only to five of them then following query will return only five issues:
When John can access only to three of fifteen projects in your JIRA, then following query will return only three projects:
The same is for all views available in Smart-QL for querying:
The same goes to filters and other Jira objects: