It's possible to disable snmptrapd running as
an AgentX subagent when compiling the code
("configure --disable-snmptrapd-subagent").
But there doesn't seem to be a way of turning this
feature off at run-time, if it's been compiled in.
It would be sensible to support a '-X' flag
(and corresponding config directive) to set the
'agentx_subagent' variable to 0.
See https://sourceforge.net/p/net-snmp/patches/1247/ . I even picked the same command line option.
This has been implemented on the 5-7-patches branch and trunk