The two weekly bonuses (for kingdom or troop type) have always applied in the Arena. That’s not a bug and never has been, so far as I can tell.
As for the shiny troops? I have noticed that on occasion, at least for the handful of troops that I have scrounged up enough shiny tokens for the upgrade to hit. That being said, I have no idea if that was intended or if it’s just one of those things that happened from slapdash programming.
I have no shiny troops. It’s always the opposing team that has the shiny troop. I have had a chance to draft one, though I chose a different troop instead. Either way, I thought the Arena was supposed to be played on an even playing field, which means no bonuses, shinies, etc. I made a topic here about the shiny troops (which I didn’t know were shiny at the time).