Wave soldering of PCB with Through hole and test points. Masking test points
You can ask the assembly house to put Kapton tape over the test pads if you've designed the PCB to make that easier. 

You can get the board supplier to add peelable solder mask, but it will cost money. 

You can just use the pogo pins on the solder covered pads in most cases, maybe not for very low level measurements, and even for those there are particularly aggressive pins available that have a drilling action.