Assuming you actually want/need to run node *as a service*, it looks like your best bet is the module that this stackoverflow answer links to:
http://stackoverflow.com/a/20724855.
If you were to write something like that yourself, from scratch, you could follow the advice in
this thread and write a simple service in C# (google "C# create service" for examples) and have that start your node.js process (google "C# start process" for examples). But it looks like someone has already done that work (or something similar, but written in node directly), as mentioned in the stackoverflow answer in the above paragraph.
It's worth mentioning that the node.js exe file is standalone, it can be "installed" on a system by simply copying the file over.
If you need it to run on startup and you don't care whether it runs as a service or not (services are trickier to get setup, but they are more bulletproof; they start running even before the user logs in and they continue running between user sessions), the simpler approach is to make a batch file that runs your node script with the node executable and to put that batch file in the user's startup/autostart folder, as mentioned in the other stackoverflow answers.
As far as the innosetup details, you'll need to do some googling to figure out the exact syntax to copy files or put them in the user's startup folder, etc. If you do decide to create a windows service, it looks like googling "innosetup service" yields some examples of how to configure innosetup to install the service.
-- peter