It is a de facto standard: you can tell because the author of that post suggests rolling your own simpler data format as an alternative.

There are indeed a lot of reasons not to use HDF5: if you have a lot of small records, are primarily storing strings, or you don't share your data with many colleagues, there are a lot of better alternatives. But if you just want to dump a few hundred GB into one massive file and have decent IO in a format people can figure out, it works pretty good.