Both packages install many files that are the same by path/name, but different by usage. IMHO, the system is supposed to have only one of them, but not both. It's easy to fix by adding to RDEPEND in both ebuilds: !virtual/snmp P.S. Alternatively, merge ebuild folders of both packages as the net-snmp version line is actually just a new version of the old ucd-snmp one and they are not supposed to have the same version numbers. ... Or are they?
Fixed in latest cvs. Please give net-snmp-5.0.9-r1 a try.