as long as you don’t complain about hestia not working like you expect it or wish for - you can host whatever you like in parallel 
there shouldn’t be warnings in nginx anyway or you are already on the path of messing things up.
hestia plus node.js might not work so well together especially if you try to merge it to far or if you don’t know what you are doing at all 
that said:
- run your node.js server outside of hestias/users home folder and use a domain only for setting up the proxy.
- don’t mess with the default configs.
- DON’T MESS WITH THE DEFAULT CONFIGS.
- rather use custom confs to be included for your proxy setup or create individual web templates that do nothing else than proxying to your node.js server