I have yet to see any that influence the appearance of the ship.
[Edited by singlerose, 1/24/2010 12:23:55 PM]
The whole idea of upgrades and the side quests based on getting your team to be loyal is for them to live through the endgame, it is possible to save all of your crew and have them get through the collector lvl at the end.
I've seen, guns, armour, shields, medbay, and scanner upgrades specifically for the SR@ Normandy.
The guns armour and shields are directly mentioned in the cutscene fighting the collector ship through the red relay (soz forgot what they call it in game), with Seth Green saying, Im glad we have these new guns, and Miranda commenting on the shields when you get hit a couple times saying they're better than the old ones and you'd be dead withouth them.
As for the Scanner you seem to find more RICH (as in massive spikes) than the normal one, they also seemed to pop into the research field randomly for the ship ones although i could be wrong.
I am not sure the scanner makes it easier to find nodes, the best thing you can do is turn of the music, as i wasn't exploring much before i got the scanner upgraded, i therefor can't say if your able to find element zero before you get it although i didnt see any on planets, only from boxes in the 3rd person areas until after i'd gotten the scanner update. I need to go through and find more of the guns as i completed the game with the 2nd of each type, and although i'd upgraded i want the better looking models you could get which are still in the pak file.
[Edited by Greyfury, 1/24/2010 9:40:50 PM]