Just a thought...
Would it not be better to move mozilla-nss into it's own sub-directory and add that to ld.so.conf above the seamonkey one rather than have duplicated entries for the default dirs?

I don't think so. It's not just about mozilla-nss, it's that having the paths in /etc/ld.so.conf searched before the main library paths doesn't seem correct. IMHO, it violates the Principle Of Least Astonishment.

The only way around it is to list those paths first in /etc/ld.so.conf. Of course, we could also remove the default paths from the loader binary, but I don't think we should since we would lose a valuable fallback in case /etc/ld.so.conf is ever misconfigured.

Fair enough. :)

You can't override anything in /lib:/usr/lib by ld.so.conf, if these paths are searched before that. So it would do exact the opposite of what people expect from /etc/ld.so.conf.

Didn't we have Mozilla in the library search path to allow other applications to use the Mozilla Gecko engine? Gecko can't be used outside Mozilla projects since years. So I think the correct approach is to remove seamonkey from ld.so.conf, because its libraries aren't meant to be used outside Seamonkey. It may even violate licenses.