The SambaServer Agent provided as bundled agent together with SF HA is not zone aware. That means when I configure the samba server process in a Solaris zone the SambaServer agent is not able to monitor it.

I experimented with setting RunInContainer = 1 for SambaServer which however can't work as SambaServerAgent is not a Script Agent, but has monitoring built into the binary. So you can consider this an RFE to make the SambaServer and corresponding agents for Samba zone aware and honour ContainerInfo.