For me, on NetBSD-6.99.31/amd64 configure says: checking whether strncat works... yes and the file isn't compiled for me. What platform are you on, and why doesn't it find strncat there?
It's an amd64 system running netbsd-6 from 20-January-2014 with pkgsrc from 8-February-2014. I just cleaned everything, re-CVSed and tried again and got the same results.
For fun I tested it on another amd64 system and got the same results. And on evbarm running netbsd-6 updated recently (I updated everything recently because of the various security advisories).
Thanks, John