File-action nodes are for report generation purposes. They are not invoked on normal object read/write.
By the looks of file size increase for the combined function node it seems there is not much benefit combining other non-function nodes into a function node. But yes care should be taken to reduce msg cloning.
On InfluxDB , I have used proper data retention policies and also down-sampling. So InfluxDB size is under control.
I think all the general things I can come up with have now been covered. I'd say that you have one option remaining and that would be to take some/all of your function nodes and convert them to native node.js modules where feasible. Not sure even that would have a major difference if consuming them still in Node-RED but the next step would be to take some discrete flows from Node-RED and translate to stand-alone node.js apps so that you didn't have all the overheads that make it so useful and easy to use but add lots of overheads.