At the moment, when making a filter using the Advanced Search, the saved filter will remove the extra bracket if it's not needed. For example, let say the filter is originally:

(Project = DEMO AND (status = Open OR Assignee = "admin"))

The above filter will be saved as:

Project = DEMO AND (status = Open OR Assignee = "admin")

There is a reason why a user intentionally adds the additional bracket on the query, so that future changes on the JQL query will be easier.

Another Example, such as complex JQL query is:
Before the filter is saved:

After the query is saved into a filter: