Many of the items and armour cause player to 1 shot people when its being used. Also they bypass any protection system running (Worldguard, faction), godmode and creative mode.

I can see in the version information that in 3.0
"Fix - damage values"
Is this a planned fix for this or is it taking about or item ID damage values?

There's no way for us to prevent players from getting hurt or affected in protection regions without hooking those plugins. We don't want to do that as it would add lots of weight to the plugin.

God mode is the same thing. We can't really check for other plugins' God modes without hooking them.

We can do creative mode, however.