Enterprise Manager 12.1.0.4 has now been released for a few weeks, as well as the 12.1.0.4 OMS Bundle patches (also known as System patches). If you plan to apply these bundle patches to your 12.1.0.4 OMS, and you are concerned about the downtime, then, you can reduce the downtime by referring to this whitepaper that contains patching instructions to reduce downtime.
Check this article on Oracle’s blog on EM Reducing Downtime While Patching Multi-OMS Environments