I believe you could still get Anima, as I think the game records having opened the chests, not having the objects in possession. For example, in some of the temples the reward in the Cloister of Trials is a sphere, such as a luck sphere, if you've used this item I don't think it would stop you from getting Anima. Though you'll just have to try and see.

The Magus Sisters have nothing to do with the Trials and are dependant on your acheivements in the Remiem Temple and the Monster Arena, so even if you can't obtain Anima, these are still available.

Don't worry, you don't need the extra Aeons to defeat the final boss. The first time through I had only the Aeons that you are awarded automatically. Also, as the first time through a game I'm more concerned about plot development than stat building, my characters were terribly weak in the final battle. Not one could hit for 9,999. All I did was haste the party of my choice and get Rikku to use 2 x Door To Tomorrow in her overdrive. As this means every hit is worth 9,999 then the boss is down in 6 hits. Disappointingly easy. If you need Doors To Tomorrow then you can steal 10, twice over, from Ultima Weapon at Omega Ruins.