Nope, no April fools from Apple, this really is an update having like 35 MB (depends on devices).
The update actually claims to contain (allegedly) the fix for the serious BUG introduced by Apple with iOS 9.3's release on March 21 (Let's loop you in) Event when they actually introduced iPhone SE too.
According to some Apple forum users, this update doesn't really fix the Safari links BUG that crashes all the apps. Let's roll in…
The bug was firstly introduced by 21 March Event iOS 9.3 release and affected a big number of users. After the user opened a link in Safari, all apps got jammed. The issue appears to be triggered by the daemon liable for credentials passing through apps (the one that allow autentifications with Facebook, Twitter and so on).
This iOS 9.3.1 was released 10 days after iOS 9.3 release, on 31 March 2016. Apple did not publish a specific report about this update, nor any security changes table.
References:
http://www.forbes.com/sites/gordonkelly/2016/04/01/apple-ios-9-3-1-should-you-upgrade/
http://www.macrumors.com/2016/03/31/apple-releases-ios-9-3-1/
https://support.apple.com/en-us/HT201222
https://support.apple.com/en-us/HT206166
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