You can operate on the PDF file, there are software that can merge pages in a PDF. This is fast as its basically just a append operation to the PDF file. (you can do this with a text editor if you must). Off course you lose the features of inDesign.
On a similar note you can let the printer add the changes, or inject the change just before print, by including the data matrix in the PostScript file itself.
Making inDesign faster
The real question is could in design be made faster? Most probably the reason your merge gets slow is that you try to fit all in one pdf file. If you chunk the operation to about 250 letters per call then it would probably work out fast. So just chunk your data into pieces. Open each piece into a separately in inDesign export and move to next piece.
If you were to do this manually it would take ages. But even if you have not scripted before it takes less time to develop knowledge into scripting to get this done than doing it manually. It is after all not more than a for loop.
Other things to Consider
- Your system does not have to be faster than the system you use to output the data with.
- Once data is split consider using several machines in parallel each machine should roughly halve your speed. A competent it admin can run the script on may machines with not much problem. (annoying fact if you batch stuff in inDesign like this then the script must be run as admin or you need to have a server license of inDesign)
Anyway this is more of a question to Superuser.
PS: Might be a good idea to hire somebody who knows what they are doing though.