There's already a bug for syncing this property (issue 839241), but the setting shouldn't be lost on upgrading Chrome - assuming you're referring to the in-place auto-update Chrome upgrades.  If you uninstall and re-install chrome, local settings are erased (by design).  Can you clarify what you mean?

I mean the in place auto upgrading Chrome, as I am using Canary, this happens a lot...

Hmm... that definitely shouldn't be happening.  We do persist a preference for the number of extensions to show in the toolbar ("extensions.toolbarsize"), and this shouldn't be rewritten on updates.  Are you also signing out/into chrome for this to happen?  (Even that, I wouldn't expect to necessarily affect this...)

It would be interesting to see what the values of the preferences are before/after updates, especially if this manifests without any sign-in state change.  If it happens on every Canary update, can you take a look at chrome://prefs-internals and search for "toolbarsize", and see what the values are before/after?

Sure, I will record the numbers before/after Chrome update upon the next Canary release, and followup on this thread. Thanks, Devlin!

Just tested, the extensions hide/show is persistent after in place upgrade, sorry mixed the sign in/out part in the bug reporting. 
Looking forward to making this a synced preference!