The only item there should be "duplicates" of, as far as I am aware, are the extra energy tanks. In terms of percentage, missiles and energy tanks are calculated based on how many you've picked up. Other upgrades are simply based on whether you have them, given that in theory there is only one place that you can obtain them and all instances of them would disappear once you have them anyways.
I thought somebody put together a complete map including all pickups.
As far as easter-eggs, God, there are too many for me to keep track of. Grimlock would probably be able to help there.