Sorry, I don't fully understand your setup or the problem.
Seems like it's modbus <--> node-red <--> MQTT <--> HASS?
But you want to cut out node red? So if the input to MQTT is slow, what's writing that MQTT value?
Without having any more context, I think I'd reach for Wireshark/tcpdump and just see the packets come in and understand timing.
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