Hi,
We have been testing with both HDD and SSD for a long time but haven't seen this before, nor do we have such reports from customers. Exporting and (especially) indexing do indeed stress the storage system -- but 40k items is a fairly small data set, our test usually involve millions of items.
I'm inclined to think this is either a hardware, driver, firmware or temperature issue. You mentioned that you are seeing the same issue on multiple machines: do all of these have identical configurations, or have relevant hardware in common? This includes: SSDs, disk controllers and motherboards. Might be worth running a disk stress test using a tool like HD Tune, while keeping an eye on SSD temperatures.