There were two builds of 9.3 (different build numbers), the last one addressing the iPad 2 activation and locking issues (build 13E237 as I recall). Then came 9.3.1 about a month ago resolving a links issue that affected many iOS devices. I keep up with this forum regularly and I have not been seeing any unusual issues with iPad 2s for a while, just back to the normal. I did see tons of issues at the time of the 9.0 release, particularly with iPad 2s. So I am surprised to hear that the Apple Store was saying not to update 10 days ago.
What version of iOS are you running on the iPad that was "fixed" by the Apple Store? If it is 9.3.1 build 13E238, that is the latest. I have 4 iOS devices with that version and all work well (but no iPad 2s). If you want to be absolutely safe do not update unless you really want one of the newer features. If it was me I would update but then again I know how to restore it in case of issues.