I tested "issueLinkType is EMPTY" and I can see Subtask are being included in the result.
If you would like to exclude Subtask from the result, you can use the following JQL:
issueLinkType is EMPTY and issuetype not in subtaskIssueTypes()
If you are still getting results that include linked issues, please provide some samples for troubleshooting.
I tried the same JQL as you mentioned above.
But here the Linked issues are not subtasks, there are linked to other projects in the same instance.
After using the JQL, we can see the linked issues in the Links Column.
Please have a look of the screenshot, my idea is to get tickets of project "A" for which they are not linked to issues in any other project B, C, D of the same instance
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