Yes. You see the visual basic(VB) application programming interface (API). Is not actually a VB only interface. It would be much better to call it a COM API*. Now every conceivable language that runs on windows has pretty efficient and free COM bridge (except Java).
Now since COM is one of those core components of Microsoft its not terribly surprising that it can be called out of PowerShell, no problem. If you prefer to use c#, python, ruby or you name it it's still not a problem.
There is just one hitch! Technically, your license of inDesign forbids you to do this on a server unattended**. So they have purposely crippled the API so that it has to be run with administrator privileges for full working functionality*** . Also you need to bake in human interaction so no timed/event based jobs, if you want to avoid Adobe skinning your business alive. So, no launching from a web page unless you want to buy InDesign Server. Neither Photoshop nor illustrator have this restriction by the way, both which can also be made to do this.
With that out of our way lets get started.
# warning: Due to licensing restriction running this code on a
# server untended is a license violation, launching it manually
# is not a problem though.
$ind = New-Object –ComObject InDesign.Application;
$doc = $ind.Open('d:\\temp\\test.indd');
# get the merged document
$merged = $ind.ActiveDocument;
Programming in powershell can be a bit clunky as it does not auto-load the constants but c'est la vie. (1952403524 = idPdfType)
On the other hand, you could just use a free XSL-FOP. Which is basically what indesign server is.
* Yeah, Microsoft chooses names so they are ungooglable.
** Because they sell a product called inDesignServer which is just a headless inDesign (for your usecase 12,300$ a year). Getting caught is really nasty as now adobe holds all cards! Make sure you annotate clearly that people do not use this in automated processes if you use this without inDesignServer.
*** Mostly xml stuff. This may be a problem if you have a big organization