Apple hasn't shed any light on its plans for security but you can expect the iOS 9.3 change log to include security updates.
iOS updates, particularly large ones like iOS 9.3, almost always come with security patches for potential exploits. If you want to look at a bit of history, go back in time and look at every iOS update between the iOS 8.1 release and the iOS 9.2 update. Only one iOS release in the middle of those two upgrades failed to bring security patches with it. That update? iOS 9.0.1, a minor update that rolled out immediately after iOS 9.0. It would be strange, and rare, to see iOS 9.3 roll out without any security patches. Apple works hard to maintain a high standard of security for enterprise users and others and we don't expect a let down here with its next big upgrade.
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