The shelf life statements are essentially to prevent mishandling of the product and not storing it properly. If the modules are still sealed in the package, stored at the proper temperature and have not been exposed to moisture they should be fine. However, when working with modules beyond their shelf life you MUST bake the modules before populating the them to your board. Failure to bake the modules could result in the yield rate dropping down lower than expectation due to popcorn or de-lamination on the modules. It is recommended that you follow IPC/JEDEC J-STD-033 which is the general standard for the handling, packing, shipping and use of moisture/reflow sensitive surface mount devices.
Our main concern is around the castellation/pads which solder the module to the board. It is imperative those pads do not get tarnished, as this would cause soldering issues. Humidity can affect solderability as well, as if there is any excess moisture in the solder on the module, during reflow of the module to the board, steam balls can essentially explode the solder and sometimes result in an open circuit (or possibly a short circuit).
As long as all of the moisture handling and temperature guidelines are being followed you will likely have no issues. It is further recommended that when you do the build with modules that have exceeded their shelf life that you start with a handful to perform a test run and do a final test to make sure all is working as expected. As long as there are no issues with the initial test run we would expect that you will not experience any problems.