Funny, just after I posted my query, I saw at the bottom another post from July 13, 2015
"iphone restart after pressing volume button".
There someone asked if StatusHUD2 was installed and it turns out that I had that tweak also
installed. I removed it and sim sala bim the volume buttons work fine again.
I search through this forums with almost everything I could think of but that post didn't show up
until after I posted mine. I was almost sure I wasn't the first to have this problem but anyway it
is fixed and I'm happy now.
Yeah, StatusHUD is still waiting for an iOS 9 update, let alone 9.3.3.
Generally the best way to troubleshoot something like this is to think about what tweak might be related.
For instance, your problem was with the volume up and down button. I wouldn't be looking through my list of tweaks thinking that Callbar or Eclipse 3 or Couria or so on would be causing this. I'd be looking for something related to volume or sound because that's what is being affected. StatusHUD or some other volume/sound related tweak would have been the one I checked.
When you really have nothing to go on this kind of thinking can really help.
Cydia also has a recents tab and will show in chronological order which tweaks you have installed/updated. It's always best if you start having an issue shortly after installing a tweak to focus on the recent tweaks. In your case this might not have helped as I guess StatusHUD wasn't a recent install.
By the way. Was it really a reboot or just a respring? I know when StatusHUD was causing issues for me it was causing resprings not reboots.