I have the same problem using FreeNAS-9.3-STABLE-201501162230 (intial install FreeNAS 9.3 release). I know this was a bug in v9.3beta when using the webui via HTTPS protocol but I don't think that's the issue here as the plugin tree menu worked initially. Switching to HTTP didn't help.
I installed transmission (only plugin), had a look at the plugins option screen then added storage at which point the icon in the tree menu disappeared. From the logs
freenas manage.py: [plugins.utils:92] Couldn't retrieve
http://192.168.1.33/plugins/transmission/1/_s/status: No JSON object could be decoded
I restored a previous configuration but ended up in the same position.
Edit: I don't have the same problem as sdgenxr. I use static IPs and changing the inital jail IP address was causing the problem which restarting jail or rebooting fixed. Yes, I'm berk for not trying that straight away instead of restoring. Note to self: Don't be a berk in future :)