Im not necessarily against the idea of having a emoncms mqtt topic that accepts json format including a timestamp. I think its one suggestion I proposed early on 
From what I understood the downside is that it makes subscribing to topics and using topics outside of emoncms, e.g by other applications such as nodered and openhab harder as they would then need to decode the json sent from say emonhub.
Im sure a modification could be made to emoncms/scripts/phpmqtt_input.php to accept both approaches if there was the desire to have this option. Happy to accept a pull request that would support both.
@borpin this sounds like the ongoing issue, for some reason I thought we where further with it?
- community.openenergymonitor.org/t/newly-created-inputs-not-appearing-in-emoncms-via-mqtt/2515/40
- community.openenergymonitor.org/t/emonbase-no-inputs-problem-with-mqtt/1698
Are you able to replicate the issue above reliably? that would be a great place to start with getting to the bottom of it?