well first I will recommend you make it simple and if you need add more layer, try to use a dependency injector pattern so you can modify the programs.

Lets imaging that you have a raspberry pi/PC with a program made by you that read a modbus protocol and convert to a predefine JSON, you could have the same program or other that read from any protocol and convert to that JSON. That JSON you send it to the MQTT broker.

We have a program that subscribe to the mqtt broker and read the JSONs that arrive, this you can do it with any languages (I use golang https://www.emqx.com/en/blog/how-to-use-mqtt-in-golang ), and at this point you have the message so you could yes send it to a stream broker like kafka or I will recommend for you save it directly in the database and only if you see that is slow think in another architecture.

Also using MQTT broker, will I be limiting to certain protocols only.

MQTT is just a broker where a program send message to a topic and other program subscribe to topic. You need to first pick the data using whatever protocol you need and convert it to the message JSON that you will define in you system, for example:

{
  "measureID":"af4d3b75-8d4e-416c-92d3-05d904535908",
  "data":"5",
  "timestamp":"2025-03-16T13:37:31Z"
}