2. Consider just trying the trees together with symlinks (Use "find" to recurse, then ln -s"). Unless you have many tens of thousands of small files, this will work remarkably well, especially if the disk that holds the symlinks is fast and has a sensible filesystem; you could even make it a ramdisk.
This seems like the most reasonable solution to me. I think people are getting caught up treating this like a high availability fileserver when it's really just a data acquisition project. Configure the disks to automatically mount, and then use a really simple condition to figure out which mounted disks have data on them (for example, the existence of a directory, or even just the size of the disk). Use a shell script to test this condition and then make symlinks for all of the data files.
I don't know exactly what kind of equipment OP is working with, but some DAQ systems let you choose what size of files to divide the output into. Try choosing the largest reasonable file size to reduce the number of symlinks.
If you really think duplicate file names are unlikely then simply don't worry about them. I would at least have the script make some sort of log so you can figure out WTF happened if you find yourself missing some data. Don't worry about security -- this is a scientific project to it's safe to assume that the root password and IP address are written in sharpie on the server anyway, probably within eyesight of a window that faces a busy street. Don't listen to the people suggesting wireless telemetry instead of sneakernet, you have at least an order of magnitude more data than would make sense for such a system.