  No, it doesn't matter where the drives are. You could have a RAID 5 with disks 0/2/4 and a RAID 1 with disks 1/3. Drive Roaming is also supported, but that doesn't mean you should go swapping disks around willy-nilly. If you have a spare slot, move disk 0 to that slot.    Yes, but confirm with diagnostics - it is most likely a bad LED on the backplane.
I have a PE2900 with 0 and 1 drives on raid 1 with my OS and 2-7 on raid 5.  Yesterday I happen to notice that the leds on drive 0 were not working at all.  Openmanage shows both drives, 0 and 1 and shows everything is good.  There are no errors from anything except when I try to manually blink the drive that's not lit I get "The operation failed to complete" error.  0 and 1 drives are 250gb Dell branded enterprise drives that have been in service for about 3 years.  I have spare drives and caddies.  Should I hot swap the 0 drive that's not lit or just leave it all alone?  This server is critical  to my operation. Any help is greatly appreciated.
poweredge 2900 caddy leds not working