Both the HTTP and MQTT input methods of emoncms have the ability to use named inputs, it really depends on the method used. Take for example the HTTP input api’s, you can use named inputs (eg 'input1':123.45,'input2':67.89) or just using CSV (eg 123.45,67.89) , the former will result in inputs called “input1” and “input2” whilst the latter inputs will be “1” and “2” as emoncms uses the index+1 for the input name. These 2 methods are not currently interchangeable (See Development: Indexed Inputs) but either can be used with HTTP or with MQTT, so if you create inputs via MQTT and then switch to HTTP or vice versa, providing they use the same method and the names are the same, it will continue to update the same inputs, incoming data is processed to the same inputs depending on id’s and names etc not by delivery method. The named method can of course be made to be compatible with the csv method by using index numbers as names (eg '1':123.45,'2':67.89) although I can’t imagine why anyone would want to do that unless it was purely for compatibility, with the bulk upload api for example.
AFAIK the emonESP uses named inputs for both MQTT and HTTP.
If it has the same node name/id and input name/id then yes it would end up in the same place regardless of where it comes from or how it is delivered, whether it overwrites or not depends on other things such as input processing, feed type, interval and whether feedwriter is enabled etc.