Missing 'man' entries after upgrade
You can set an environmental variable called MANPATH that will tell the "man" command where to look for the man pages. I see my mac 10.12.6 (Sierra) does not have that variable set.  According to "man man"  output, it uses /etc/man.conf to know where the directories are. You can add missing paths into that file.  That file may be overwritten by an mac os x update, so you may have to do it again.  To find your missing man3 files, which are probably still on your disk, try "locate \*man3"  and it should list every directory with a man3 folder in it.
Boyd