Why is it necesssary to toggle this option at all? It's an instance option, not a database option - so it affects all other databases in the same instance, too.
This can lead to undesired side-effects.
Is there a way to specify this via a JDBC driver connection url property to avoid a change for the whole sql server instance?
No, it's not possible to set it in the JDBC driver - MS-SQL doesn't support it being set other than in the internal options, so the JDBC driver can't do anything about it.
This setting can affect atlassian apps, see https://confluence.atlassian.com/display/JIRA/Error+caused+by+SET+NOCOUNT+in+MS+SQL+Server for the examples of problems.
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