Just tested several Audiomoths in different housings. It is clear that disabling the LED doesn't have an impact on the clicks mentioned above. Like Andy stated, it is likely to be the writing to the SD cards. Unfortunately those clicks are much more present when put in a case. The plastic bag is intermediate and without any protection it is negligible.
Recording in tropical conditions require adding some housing. We hope this can be solved in the next batches....
Recording snippet with SD card write 'clicks' when put in a plastic housing